Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014085.1 Kokia drynarioides strain JFW-HI SEQ_129116, 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: 70345
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 80 characters in sequence are not A, C, G, or T
Found at i:8028 original size:15 final size:17
Alignment explanation
Indices: 8007--8047 Score: 59
Period size: 15 Copynumber: 2.5 Consensus size: 17
7997 TAATTTTTTA
8007 AAAATTATAAAAAT-AT
1 AAAATTATAAAAATAAT
*
8023 -AAATTATTAAAATAAT
1 AAAATTATAAAAATAAT
8039 AAAATTATA
1 AAAATTATA
8048 TTTTTATTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 12 0.57
16 2 0.10
17 7 0.33
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
AAAATTATAAAAATAAT
Found at i:16874 original size:96 final size:96
Alignment explanation
Indices: 16715--16903 Score: 342
Period size: 96 Copynumber: 2.0 Consensus size: 96
16705 GACTCGGTTA
16715 ACATTTTCCATTTTCCAGCTAAAATGGCGACTAAAATCCTTAAGAAAAGGTAGCCGCTCTTTGGG
1 ACATTTTCCATTTTCCAGCTAAAATGGCGACTAAAATCCTTAAGAAAAGGTAGCCGCTCTTTGGG
* *
16780 GTTTCAAGTTTAGACTCTGTAAATAAATTTT
66 GTTCCAAGGTTAGACTCTGTAAATAAATTTT
16811 ACATTTTCCATTTTCCAGCTAAAATGGCGACTAAAATCCTTAAGAAAAGGTAGCCGCTCTTTGGG
1 ACATTTTCCATTTTCCAGCTAAAATGGCGACTAAAATCCTTAAGAAAAGGTAGCCGCTCTTTGGG
* *
16876 GTTCCAAGGTTAGATTTTGTAAATAAAT
66 GTTCCAAGGTTAGACTCTGTAAATAAAT
16904 CTGTCACGTA
Statistics
Matches: 89, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
96 89 1.00
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Consensus pattern (96 bp):
ACATTTTCCATTTTCCAGCTAAAATGGCGACTAAAATCCTTAAGAAAAGGTAGCCGCTCTTTGGG
GTTCCAAGGTTAGACTCTGTAAATAAATTTT
Found at i:28403 original size:4 final size:4
Alignment explanation
Indices: 28394--28420 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
28384 GTTTGAACAA
28394 TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TAT
28421 TCAAGTCTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.22, T:0.52
Consensus pattern (4 bp):
TATG
Found at i:42429 original size:14 final size:15
Alignment explanation
Indices: 42412--42446 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
42402 TAAAAACATT
*
42412 AAAATAAAC-ATTTA
1 AAAATAAACGAATTA
42426 AAAATAAACGAATTA
1 AAAATAAACGAATTA
42441 AAAATA
1 AAAATA
42447 CATTAAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 9 0.47
15 10 0.53
ACGTcount: A:0.69, C:0.06, G:0.03, T:0.23
Consensus pattern (15 bp):
AAAATAAACGAATTA
Found at i:42653 original size:22 final size:22
Alignment explanation
Indices: 42628--42677 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
42618 AAATAACGGC
42628 AAAACAA-CAACAAAAACAGTAA
1 AAAACAAGC-ACAAAAACAGTAA
* *
42650 AAAAAAAGCACTAAAACAGTAA
1 AAAACAAGCACAAAAACAGTAA
42672 AAAACA
1 AAAACA
42678 GTAATATAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 23 0.96
23 1 0.04
ACGTcount: A:0.72, C:0.16, G:0.06, T:0.06
Consensus pattern (22 bp):
AAAACAAGCACAAAAACAGTAA
Found at i:43043 original size:20 final size:20
Alignment explanation
Indices: 43014--43072 Score: 66
Period size: 20 Copynumber: 2.9 Consensus size: 20
43004 CCTTGAACAA
*
43014 GTTCGAATTCG-AGATTTAAG
1 GTTCGGATTCGAAG-TTTAAG
43034 GTTCGGATTCGAAGTTTAAG
1 GTTCGGATTCGAAGTTTAAG
* *
43054 GCTCGGAGCTCGAAGTTTA
1 GTTCGGA-TTCGAAGTTTA
43073 GAGTTTAGGA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
20 22 0.65
21 12 0.35
ACGTcount: A:0.25, C:0.14, G:0.29, T:0.32
Consensus pattern (20 bp):
GTTCGGATTCGAAGTTTAAG
Found at i:48256 original size:2 final size:2
Alignment explanation
Indices: 48249--48273 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
48239 ATATTTTGTC
48249 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
48274 AACAACCCAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:54019 original size:7 final size:7
Alignment explanation
Indices: 54007--54031 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
53997 TTGTTATAAT
54007 TATATTA
1 TATATTA
54014 TATATTA
1 TATATTA
54021 TATATTA
1 TATATTA
54028 TATA
1 TATA
54032 CATATTGAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (7 bp):
TATATTA
Found at i:55473 original size:12 final size:12
Alignment explanation
Indices: 55440--55481 Score: 57
Period size: 12 Copynumber: 3.4 Consensus size: 12
55430 TTTCCAACTA
*
55440 ATAAAGATTAGT
1 ATAAAAATTAGT
*
55452 ATAAATAATTATT
1 ATAAA-AATTAGT
55465 ATAAAAATTAGT
1 ATAAAAATTAGT
55477 ATAAA
1 ATAAA
55482 GGAGAAGGCA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
12 16 0.62
13 10 0.38
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.36
Consensus pattern (12 bp):
ATAAAAATTAGT
Found at i:61718 original size:5 final size:5
Alignment explanation
Indices: 61708--61738 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
61698 AATATCTCTC
61708 TCTTT TCTTT TCTTT TCTTT TCTTT TCTTT T
1 TCTTT TCTTT TCTTT TCTTT TCTTT TCTTT T
61739 TTTAAAGAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TCTTT
Found at i:64840 original size:30 final size:30
Alignment explanation
Indices: 64804--64868 Score: 121
Period size: 30 Copynumber: 2.2 Consensus size: 30
64794 CAACTTAATA
*
64804 AACAAATGTCTCTAAAATAATAACAAAATT
1 AACAAATGCCTCTAAAATAATAACAAAATT
64834 AACAAATGCCTCTAAAATAATAACAAAATT
1 AACAAATGCCTCTAAAATAATAACAAAATT
64864 AACAA
1 AACAA
64869 TAAAATAAGT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.58, C:0.15, G:0.03, T:0.23
Consensus pattern (30 bp):
AACAAATGCCTCTAAAATAATAACAAAATT
Done.