Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008664.1 Kokia drynarioides strain JFW-HI SEQ_123346, 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: 53888
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.34
Warning! 31 characters in sequence are not A, C, G, or T
Found at i:4331 original size:22 final size:21
Alignment explanation
Indices: 4307--4346 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
4297 TTAACGTAGT
4307 TTTTCTATATTTTCCATTTAG
1 TTTTCTATATTTTCCATTTAG
4328 TTTTCTATATTTTCCATTT
1 TTTTCTATATTTTCCATTT
4347 GTCAAAACTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.17, C:0.15, G:0.03, T:0.65
Consensus pattern (21 bp):
TTTTCTATATTTTCCATTTAG
Found at i:15867 original size:12 final size:12
Alignment explanation
Indices: 15810--15899 Score: 55
Period size: 12 Copynumber: 7.8 Consensus size: 12
15800 ATAACATCTA
15810 AACAACAAAAAT
1 AACAACAAAAAT
*
15822 AACAATC-AAAAC
1 AACAA-CAAAAAT
* **
15834 AGCAGTAAAAAT
1 AACAACAAAAAT
* *
15846 AATAA-TAAAAT
1 AACAACAAAAAT
15857 AACAAC--AAA-
1 AACAACAAAAAT
15866 AACAACAAAAAT
1 AACAACAAAAAT
* *
15878 AGCAACAAAACT
1 AACAACAAAAAT
*
15890 AACAGCAAAA
1 AACAACAAAA
15900 CAACACCAAA
Statistics
Matches: 58, Mismatches: 14, Indels: 12
0.69 0.17 0.14
Matches are distributed among these distances:
9 6 0.10
10 3 0.05
11 12 0.21
12 36 0.62
13 1 0.02
ACGTcount: A:0.69, C:0.17, G:0.04, T:0.10
Consensus pattern (12 bp):
AACAACAAAAAT
Found at i:15959 original size:19 final size:20
Alignment explanation
Indices: 15937--15990 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 20
15927 TCAAAACGCA
*
15937 ACCAAAATAGTAAAAA-AAT
1 ACCAAAATAGTAAAAATAAC
*
15956 ACCAAAACAGTAAAAAATAAC
1 ACCAAAATAGT-AAAAATAAC
15977 ACCAAAATAG-AAAA
1 ACCAAAATAGTAAAA
15991 GAAAAAAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
19 14 0.47
20 5 0.17
21 11 0.37
ACGTcount: A:0.69, C:0.15, G:0.06, T:0.11
Consensus pattern (20 bp):
ACCAAAATAGTAAAAATAAC
Found at i:15972 original size:21 final size:21
Alignment explanation
Indices: 15948--15997 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
15938 CCAAAATAGT
* *
15948 AAAAAAATACCAAAACAGTAA
1 AAAAAAACACCAAAACAGAAA
* *
15969 AAAATAACACCAAAATAGAAA
1 AAAAAAACACCAAAACAGAAA
15990 AGAAAAAA
1 A-AAAAAA
15998 AAAACATCAA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
21 18 0.78
22 5 0.22
ACGTcount: A:0.74, C:0.12, G:0.06, T:0.08
Consensus pattern (21 bp):
AAAAAAACACCAAAACAGAAA
Found at i:20247 original size:2 final size:2
Alignment explanation
Indices: 20240--20266 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
20230 TTCTTTAAAT
20240 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
20267 GAGGAATGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:39564 original size:2 final size:2
Alignment explanation
Indices: 39507--39546 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
39497 CTTCACAAAC
*
39507 AG AG CG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
39547 CGAAAAAGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.47, C:0.03, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:39674 original size:5 final size:5
Alignment explanation
Indices: 39664--39689 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
39654 CTCTTTCCAA
39664 GCCAT GCCAT GCCAT GCCAT GCCAT G
1 GCCAT GCCAT GCCAT GCCAT GCCAT G
39690 TTGAAGAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.38, G:0.23, T:0.19
Consensus pattern (5 bp):
GCCAT
Found at i:40951 original size:14 final size:13
Alignment explanation
Indices: 40926--40959 Score: 59
Period size: 14 Copynumber: 2.5 Consensus size: 13
40916 GTTTATTTCA
40926 CTGAAAATGATTT
1 CTGAAAATGATTT
40939 CTGAAACATGATTT
1 CTGAAA-ATGATTT
40953 CTGAAAA
1 CTGAAAA
40960 ATTATTTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 7 0.35
14 13 0.65
ACGTcount: A:0.41, C:0.12, G:0.15, T:0.32
Consensus pattern (13 bp):
CTGAAAATGATTT
Found at i:40966 original size:14 final size:14
Alignment explanation
Indices: 40929--40966 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
40919 TATTTCACTG
40929 AAAATGATTTCTGA
1 AAAATGATTTCTGA
*
40943 AACATGATTTCTGA
1 AAAATGATTTCTGA
*
40957 AAAATTATTT
1 AAAATGATTT
40967 ATTTTTTGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.42, C:0.08, G:0.11, T:0.39
Consensus pattern (14 bp):
AAAATGATTTCTGA
Found at i:43728 original size:23 final size:23
Alignment explanation
Indices: 43684--43729 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
43674 AAAATTTTCA
* **
43684 AAAATTGAAAACAAAAGTCTTTT
1 AAAATTGAAAAAAAAAAACTTTT
*
43707 AAAATTTAAAAAAAAAAACTTTT
1 AAAATTGAAAAAAAAAAACTTTT
43730 TTTAATTTTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.59, C:0.07, G:0.04, T:0.30
Consensus pattern (23 bp):
AAAATTGAAAAAAAAAAACTTTT
Found at i:43991 original size:22 final size:22
Alignment explanation
Indices: 43935--43991 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
43925 TTGCATCAAA
*
43935 AAAAATAAATATGATCAAAATC
1 AAAAATAAATATTATCAAAATC
* *
43957 TATAATAAA-ATTATTCAAAAT-
1 AAAAATAAATATTA-TCAAAATC
43978 AAAAATAAATATTA
1 AAAAATAAATATTA
43992 ATTAAATTAC
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
21 10 0.36
22 18 0.64
ACGTcount: A:0.63, C:0.05, G:0.02, T:0.30
Consensus pattern (22 bp):
AAAAATAAATATTATCAAAATC
Found at i:45015 original size:63 final size:64
Alignment explanation
Indices: 44947--45075 Score: 215
Period size: 63 Copynumber: 2.0 Consensus size: 64
44937 AAACCTAAAT
*
44947 ATTATGATTTTTATCGGATGTCATTTTAGTTAACGAGT-CACAATTTTATTTTTTTCTCTTGAA
1 ATTATGATTTTTATCGGATGTCATTTTAGTTAACGAGTCCACAATTTTATTTTTCTCTCTTGAA
** *
45010 ATTATGATTTTTATTTGATGTCATTTTAGTTAGCGAGTCCACAATTTTATTTTTCTCTCTTGAA
1 ATTATGATTTTTATCGGATGTCATTTTAGTTAACGAGTCCACAATTTTATTTTTCTCTCTTGAA
45074 AT
1 AT
45076 ATGTTTAATT
Statistics
Matches: 61, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
63 35 0.57
64 26 0.43
ACGTcount: A:0.25, C:0.12, G:0.12, T:0.51
Consensus pattern (64 bp):
ATTATGATTTTTATCGGATGTCATTTTAGTTAACGAGTCCACAATTTTATTTTTCTCTCTTGAA
Found at i:49768 original size:21 final size:23
Alignment explanation
Indices: 49717--49768 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 23
49707 AGAGAGTTAA
49717 ATTTAATAAAATAGTATGGATGTGT
1 ATTTAATAAAATAGTAT-G-TGTGT
49742 -TTTAATAAAATA-TAT-TGTGT
1 ATTTAATAAAATAGTATGTGTGT
49762 ATTTAAT
1 ATTTAAT
49769 TCCGTAGCTG
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
20 5 0.19
21 6 0.23
23 3 0.12
24 12 0.46
ACGTcount: A:0.40, C:0.00, G:0.13, T:0.46
Consensus pattern (23 bp):
ATTTAATAAAATAGTATGTGTGT
Done.