Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004678.1 Kokia drynarioides strain JFW-HI SEQ_118228, 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: 74164
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.34
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:1766 original size:24 final size:25
Alignment explanation
Indices: 1713--1766 Score: 58
Period size: 24 Copynumber: 2.2 Consensus size: 25
1703 GGAGCCTTGC
1713 AAACAAACTATATGGACAATAGACA
1 AAACAAACTATATGGACAATAGACA
* * *
1738 CAACAAAC-ATTTGGACTATCA-ACA
1 AAACAAACTATATGGACAAT-AGACA
1762 AAACA
1 AAACA
1767 GTTAGGGAAG
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
24 16 0.67
25 8 0.33
ACGTcount: A:0.54, C:0.20, G:0.09, T:0.17
Consensus pattern (25 bp):
AAACAAACTATATGGACAATAGACA
Found at i:15925 original size:23 final size:23
Alignment explanation
Indices: 15863--15937 Score: 84
Period size: 23 Copynumber: 3.3 Consensus size: 23
15853 AAGTATTTAA
15863 CAGTAAGCACACACAGTGC-AAT
1 CAGTAAGCACACACAGTGCAAAT
* * *
15885 CAGTAGGCGCACATAGTGCAAAT
1 CAGTAAGCACACACAGTGCAAAT
15908 CAGTAAGCACACGA-AGTGCGAAA-
1 CAGTAAGCACAC-ACAGTGC-AAAT
15931 CAGTAAG
1 CAGTAAG
15938 TGCACTAGCG
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
22 16 0.36
23 25 0.56
24 4 0.09
ACGTcount: A:0.40, C:0.23, G:0.24, T:0.13
Consensus pattern (23 bp):
CAGTAAGCACACACAGTGCAAAT
Found at i:19502 original size:57 final size:57
Alignment explanation
Indices: 19435--19550 Score: 214
Period size: 57 Copynumber: 2.0 Consensus size: 57
19425 AATTTAAAAG
*
19435 TTCAACTATTAATTTTGTTCCGAACATAGCAAGCATTCGTAATCTTTTTATTTTTGT
1 TTCAACTATTAATTTAGTTCCGAACATAGCAAGCATTCGTAATCTTTTTATTTTTGT
*
19492 TTCAACTATTAATTTAGTTCCGAACATATCAAGCATTCGTAATCTTTTTATTTTTGT
1 TTCAACTATTAATTTAGTTCCGAACATAGCAAGCATTCGTAATCTTTTTATTTTTGT
19549 TT
1 TT
19551 AGGGTTGTAA
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
57 57 1.00
ACGTcount: A:0.27, C:0.16, G:0.09, T:0.48
Consensus pattern (57 bp):
TTCAACTATTAATTTAGTTCCGAACATAGCAAGCATTCGTAATCTTTTTATTTTTGT
Found at i:44399 original size:7 final size:8
Alignment explanation
Indices: 44386--44416 Score: 62
Period size: 8 Copynumber: 3.9 Consensus size: 8
44376 TAAAATCATA
44386 AAAAAAAT
1 AAAAAAAT
44394 AAAAAAAT
1 AAAAAAAT
44402 AAAAAAAT
1 AAAAAAAT
44410 AAAAAAA
1 AAAAAAA
44417 CCACAACAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (8 bp):
AAAAAAAT
Found at i:56228 original size:20 final size:20
Alignment explanation
Indices: 56205--56242 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
56195 ATCTTCTAAA
56205 ATTTTGAAAAATTATAAATG
1 ATTTTGAAAAATTATAAATG
**
56225 ATTTTTTAAAATTATAAA
1 ATTTTGAAAAATTATAAA
56243 AAGTATATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (20 bp):
ATTTTGAAAAATTATAAATG
Found at i:57915 original size:49 final size:49
Alignment explanation
Indices: 57855--57953 Score: 180
Period size: 49 Copynumber: 2.0 Consensus size: 49
57845 AAATGTTTTC
*
57855 ATTGAAACAGATTGGACAGAATCAGAGGATTAACTTCGAAAATTCACTA
1 ATTGAAACAGATTGGACAGAATCAAAGGATTAACTTCGAAAATTCACTA
*
57904 ATTGAAACAGATTGGACAGAATCAAAGGATTAACTTTGAAAATTCACTA
1 ATTGAAACAGATTGGACAGAATCAAAGGATTAACTTCGAAAATTCACTA
57953 A
1 A
57954 AAATGGTATA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.44, C:0.13, G:0.17, T:0.25
Consensus pattern (49 bp):
ATTGAAACAGATTGGACAGAATCAAAGGATTAACTTCGAAAATTCACTA
Found at i:63353 original size:13 final size:13
Alignment explanation
Indices: 63337--63362 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
63327 GAAGTAATTG
63337 AATTGTTTTTAAA
1 AATTGTTTTTAAA
63350 AATTGTTTTTAAA
1 AATTGTTTTTAAA
63363 TATTTTATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (13 bp):
AATTGTTTTTAAA
Found at i:64740 original size:23 final size:22
Alignment explanation
Indices: 64691--64732 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
64681 ATAGATTTAA
64691 CATTTATTATTAAAAAAAACAT
1 CATTTATTATTAAAAAAAACAT
* *
64713 CATTTATTATTTAACAAAAC
1 CATTTATTATTAAAAAAAAC
64733 TAATATTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (22 bp):
CATTTATTATTAAAAAAAACAT
Done.