Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005108.1 Kokia drynarioides strain JFW-HI SEQ_118931, 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: 21688
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.35
Warning! 13 characters in sequence are not A, C, G, or T
Found at i:13746 original size:2 final size:2
Alignment explanation
Indices: 13733--13775 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
13723 TACTGCTCAA
* *
13733 CT CT CT CA CT CT CT CT TT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
13775 C
1 C
13776 ACACGCACTC
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.02, C:0.49, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:17963 original size:31 final size:31
Alignment explanation
Indices: 17926--18004 Score: 88
Period size: 31 Copynumber: 2.6 Consensus size: 31
17916 AAATGTGAAT
* *
17926 AATTGAATCAAAATTAAAGTTTGATGTGTAC
1 AATTGAATCAAAATCAAAGTTTGATGCGTAC
* * * *
17957 ATTTGAACCACAATCAAAGTTTTATGCGTAC
1 AATTGAATCAAAATCAAAGTTTGATGCGTAC
*
17988 AATTGCATC-AAATCAAA
1 AATTGAATCAAAATCAAA
18005 ATTCATATAT
Statistics
Matches: 38, Mismatches: 10, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
30 7 0.18
31 31 0.82
ACGTcount: A:0.42, C:0.14, G:0.13, T:0.32
Consensus pattern (31 bp):
AATTGAATCAAAATCAAAGTTTGATGCGTAC
Found at i:18595 original size:31 final size:31
Alignment explanation
Indices: 18532--18596 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
18522 CTTAACAACC
* ** * *
18532 CAATGACTTAAATAAAATTTTTTAAATGATT
1 CAATAACTTAAATAAAAACTTTCAAATAATT
18563 CAATAACTTAAATAAAAACTTTCAAATAATT
1 CAATAACTTAAATAAAAACTTTCAAATAATT
18594 CAA
1 CAA
18597 AAAAAAAAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.51, C:0.11, G:0.03, T:0.35
Consensus pattern (31 bp):
CAATAACTTAAATAAAAACTTTCAAATAATT
Found at i:20380 original size:103 final size:103
Alignment explanation
Indices: 20253--20460 Score: 407
Period size: 103 Copynumber: 2.0 Consensus size: 103
20243 TATTCATATA
*
20253 TATATATATATATATATAATGCGAAAAATTAAATTTATTGATAAATCCAAAAAGACAAGTGCACA
1 TATATATATATATATATAATGCGAAAAATTAAAATTATTGATAAATCCAAAAAGACAAGTGCACA
20318 TAATATCCCAAAGTGTAGAAGGTCTTATTCCACAAAAT
66 TAATATCCCAAAGTGTAGAAGGTCTTATTCCACAAAAT
20356 TATATATATATATATATAATGCGAAAAATTAAAATTATTGATAAATCCAAAAAGACAAGTGCACA
1 TATATATATATATATATAATGCGAAAAATTAAAATTATTGATAAATCCAAAAAGACAAGTGCACA
20421 TAATATCCCAAAGTGTAGAAGGTCTTATTCCACAAAAT
66 TAATATCCCAAAGTGTAGAAGGTCTTATTCCACAAAAT
20459 TA
1 TA
20461 ATTAGTGTAT
Statistics
Matches: 104, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
103 104 1.00
ACGTcount: A:0.47, C:0.12, G:0.11, T:0.30
Consensus pattern (103 bp):
TATATATATATATATATAATGCGAAAAATTAAAATTATTGATAAATCCAAAAAGACAAGTGCACA
TAATATCCCAAAGTGTAGAAGGTCTTATTCCACAAAAT
Found at i:20513 original size:2 final size:2
Alignment explanation
Indices: 20506--20537 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
20496 AAATACTTTC
20506 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
20538 GAAAGTTGGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:21500 original size:12 final size:12
Alignment explanation
Indices: 21491--21528 Score: 58
Period size: 12 Copynumber: 3.1 Consensus size: 12
21481 ACAAAAAATG
21491 AAGAAAAAAAGA
1 AAGAAAAAAAGA
21503 AAGAAAAAAGAGA
1 AAGAAAAAA-AGA
*
21516 AAGAAAGAAAGA
1 AAGAAAAAAAGA
21528 A
1 A
21529 GGAGAAGAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 13 0.54
13 11 0.46
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (12 bp):
AAGAAAAAAAGA
Found at i:21516 original size:21 final size:23
Alignment explanation
Indices: 21483--21528 Score: 69
Period size: 21 Copynumber: 2.1 Consensus size: 23
21473 GGGGACCAAC
21483 AAAAAATGAAGAAAAAAAGAAAG
1 AAAAAATGAAGAAAAAAAGAAAG
*
21506 AAAAAA-G-AGAAAGAAAGAAAG
1 AAAAAATGAAGAAAAAAAGAAAG
21527 AA
1 AA
21529 GGAGAAGAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 15 0.68
22 1 0.05
23 6 0.27
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (23 bp):
AAAAAATGAAGAAAAAAAGAAAG
Done.