Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003982.1 Kokia drynarioides strain JFW-HI SEQ_117085, 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: 40956
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 24 characters in sequence are not A, C, G, or T
Found at i:2944 original size:39 final size:39
Alignment explanation
Indices: 2860--2949 Score: 110
Period size: 39 Copynumber: 2.3 Consensus size: 39
2850 CACTGTTAGT
* * * *
2860 TCAGTACTGCAGTACGGTATTTACAGGGTTACTATCAGT
1 TCAGTATTGCATTACGGTATTTACAGGGTTACGATCAGC
* *
2899 TTAGTATTGCATTACGGTATTTACAGTGTTATCGA-CAGC
1 TCAGTATTGCATTACGGTATTTACAGGGTTA-CGATCAGC
2938 TCAGTATTGCAT
1 TCAGTATTGCAT
2950 CGTAGTGTTT
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
39 41 0.95
40 2 0.05
ACGTcount: A:0.26, C:0.17, G:0.21, T:0.37
Consensus pattern (39 bp):
TCAGTATTGCATTACGGTATTTACAGGGTTACGATCAGC
Found at i:3992 original size:16 final size:17
Alignment explanation
Indices: 3971--4006 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
3961 TGGTTTCCAC
3971 AAAATAAAA-AAAATAA
1 AAAATAAAAGAAAATAA
*
3987 AAAATAAAAGCAAATAA
1 AAAATAAAAGAAAATAA
4004 AAA
1 AAA
4007 GGACTTAATC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 9 0.50
17 9 0.50
ACGTcount: A:0.83, C:0.03, G:0.03, T:0.11
Consensus pattern (17 bp):
AAAATAAAAGAAAATAA
Found at i:11951 original size:10 final size:10
Alignment explanation
Indices: 11911--11963 Score: 54
Period size: 10 Copynumber: 5.2 Consensus size: 10
11901 AATTTTTCTC
11911 ATCACATATTA
1 ATCACATA-TA
*
11922 ATCACTTAT-
1 ATCACATATA
*
11931 ATCCACTTATA
1 AT-CACATATA
11942 ATCACATATA
1 ATCACATATA
*
11952 ATCACATTTA
1 ATCACATATA
11962 AT
1 AT
11964 TAAAGTTTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
9 2 0.05
10 26 0.70
11 9 0.24
ACGTcount: A:0.42, C:0.21, G:0.00, T:0.38
Consensus pattern (10 bp):
ATCACATATA
Found at i:15532 original size:22 final size:22
Alignment explanation
Indices: 15489--15532 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
15479 GTAACTATTT
* *
15489 GAAATCTGGAATCGTTGAGTCG
1 GAAATCTGAAATCGTGGAGTCG
* *
15511 GAAATCTGAAATTGTGGCGTCG
1 GAAATCTGAAATCGTGGAGTCG
15533 AGTAGAAGCA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.27, C:0.14, G:0.32, T:0.27
Consensus pattern (22 bp):
GAAATCTGAAATCGTGGAGTCG
Found at i:29704 original size:38 final size:38
Alignment explanation
Indices: 29653--29728 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 38
29643 GAATGAAGTA
29653 TGTTTTCCTTGACTTTGAAAATATCCTTGTCTTTTTAT
1 TGTTTTCCTTGACTTTGAAAATATCCTTGTCTTTTTAT
*
29691 TGTTTTGCTTGACTTTGAAAATATCCTTGTCTTTTTAT
1 TGTTTTCCTTGACTTTGAAAATATCCTTGTCTTTTTAT
29729 AGCTTTAACA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.18, C:0.14, G:0.12, T:0.55
Consensus pattern (38 bp):
TGTTTTCCTTGACTTTGAAAATATCCTTGTCTTTTTAT
Found at i:39181 original size:17 final size:17
Alignment explanation
Indices: 39143--39175 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
39133 TTATTATTTT
39143 ATTTATGTAATTTTATA
1 ATTTATGTAATTTTATA
39160 ATTTATG-AA-TTTATA
1 ATTTATGTAATTTTATA
39175 A
1 A
39176 ATTTTAAGTC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 2 0.12
17 7 0.44
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (17 bp):
ATTTATGTAATTTTATA
Done.