Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001338.1 Kokia drynarioides strain JFW-HI SEQ_112782, 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: 43995
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 41 characters in sequence are not A, C, G, or T
Found at i:11 original size:6 final size:6
Alignment explanation
Indices: 1--50 Score: 73
Period size: 6 Copynumber: 8.3 Consensus size: 6
* * *
1 CGTGGG CGTGGG CGTGGG CGTGGG CGTGGG CGAGGG CGAGGG CGAGGG
1 CGTGGG CGTGGG CGTGGG CGTGGG CGTGGG CGTGGG CGTGGG CGTGGG
49 CG
1 CG
51 AGAATGGGTT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 43 1.00
ACGTcount: A:0.06, C:0.18, G:0.66, T:0.10
Consensus pattern (6 bp):
CGTGGG
Found at i:1826 original size:19 final size:19
Alignment explanation
Indices: 1802--1838 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
1792 AAGTATAACA
1802 AATGAGGA-AGACAAGGTGT
1 AATGAGGAGA-ACAAGGTGT
1821 AATGAGGAGAACAAGGTG
1 AATGAGGAGAACAAGGTG
1839 ATGTAGTGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 16 0.94
20 1 0.06
ACGTcount: A:0.43, C:0.05, G:0.38, T:0.14
Consensus pattern (19 bp):
AATGAGGAGAACAAGGTGT
Found at i:25087 original size:17 final size:17
Alignment explanation
Indices: 25065--25104 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
25055 AAAAACCACC
* *
25065 TTTTCTTTTTCTTTTTT
1 TTTTCTTTTCCTTGTTT
25082 TTTTCTTTTCCTTGTTT
1 TTTTCTTTTCCTTGTTT
25099 TTTTCT
1 TTTTCT
25105 CCACCTTTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.00, C:0.15, G:0.03, T:0.82
Consensus pattern (17 bp):
TTTTCTTTTCCTTGTTT
Found at i:38190 original size:20 final size:21
Alignment explanation
Indices: 38167--38210 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
38157 AATACATGTC
*
38167 TTTTT-ATTTTTTTATAATAT
1 TTTTTAATTTTTATATAATAT
*
38187 TTTTTAATTTTTATATATTAT
1 TTTTTAATTTTTATATAATAT
38208 TTT
1 TTT
38211 AACTTTTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (21 bp):
TTTTTAATTTTTATATAATAT
Found at i:38197 original size:19 final size:21
Alignment explanation
Indices: 38175--38224 Score: 72
Period size: 19 Copynumber: 2.6 Consensus size: 21
38165 TCTTTTTATT
38175 TTTTTATAATATT-TTTTAA-
1 TTTTTATAATATTATTTTAAC
38194 TTTTTAT-ATATTATTTTAAC
1 TTTTTATAATATTATTTTAAC
38214 TTTTTA-AATAT
1 TTTTTATAATAT
38225 ATATATATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
18 5 0.18
19 13 0.46
20 10 0.36
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (21 bp):
TTTTTATAATATTATTTTAAC
Found at i:38218 original size:21 final size:20
Alignment explanation
Indices: 38167--38224 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 20
38157 AATACATGTC
*
38167 TTTTTATTTTTTTATAATAT
1 TTTTTAATTTTTTATAATAT
38187 TTTTTAA-TTTTTAT-ATAT
1 TTTTTAATTTTTTATAATAT
*
38205 TATTTTAACTTTTTA-AATAT
1 T-TTTTAATTTTTTATAATAT
38225 ATATATATAT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
18 5 0.15
19 13 0.38
20 16 0.47
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (20 bp):
TTTTTAATTTTTTATAATAT
Found at i:38263 original size:25 final size:25
Alignment explanation
Indices: 38233--38284 Score: 61
Period size: 25 Copynumber: 2.0 Consensus size: 25
38223 ATATATATAT
38233 ATATATATTAGAA-TTTTATAAAAAAAA
1 ATAT-TATTA-AACTTTT-TAAAAAAAA
*
38260 ATATTTTTAAACTTTTTAAAAAAAA
1 ATATTATTAAACTTTTTAAAAAAAA
38285 TACAATTTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
25 11 0.48
26 8 0.35
27 4 0.17
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (25 bp):
ATATTATTAAACTTTTTAAAAAAAA
Found at i:43294 original size:3 final size:3
Alignment explanation
Indices: 43286--43316 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
43276 TATTATGTTA
43286 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
43317 CCAACCAAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Done.