Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009657.1 Kokia drynarioides strain JFW-HI SEQ_124375, 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: 3821
ACGTcount: A:0.40, C:0.12, G:0.11, T:0.37
Found at i:72 original size:21 final size:20
Alignment explanation
Indices: 32--74 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
22 AGAAATATAT
*
32 AAAAATAAATAAATATTTTA
1 AAAAATAAATAAATAATTTA
52 AAAAATATAAT-AATAAATTTA
1 AAAAATA-AATAAAT-AATTTA
73 AA
1 AA
75 TTTTATATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
AAAAATAAATAAATAATTTA
Found at i:581 original size:27 final size:27
Alignment explanation
Indices: 550--606 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
540 TTATATTTAT
*
550 AATTTTTATTT-ATATATATTTACATAA
1 AATTTTAATTTAATATA-ATTTACATAA
* *
577 AATTTTAATTTAATTTAATTTTCATAA
1 AATTTTAATTTAATATAATTTACATAA
604 AAT
1 AAT
607 ATTGATATCG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 22 0.85
28 4 0.15
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (27 bp):
AATTTTAATTTAATATAATTTACATAA
Found at i:920 original size:21 final size:20
Alignment explanation
Indices: 894--1021 Score: 67
Period size: 21 Copynumber: 5.8 Consensus size: 20
884 AACAACACCC
894 AAACAACAAAAAGAACAGCAA
1 AAACAACAAAAA-AACAGCAA
* *
915 AAACAACAATAAAAATAACAA
1 AAACAACAA-AAAAACAGCAA
* * * *
936 AAAAATAGTAAAAATAACTGGAAAA
1 AAACA-A-CAAAAA-AAC-AG-CAA
* *
961 AAAGAAGCAAAAATAACAGTAA
1 AAACAA-CAAAAA-AACAGCAA
*
983 AAACAACAAAAACAACAGTAA
1 AAACAACAAAAA-AACAGCAA
*
1004 AAATAACAACAAAAACAG
1 AAACAACAA-AAAAACAG
1022 TATACTAACA
Statistics
Matches: 85, Mismatches: 15, Indels: 14
0.75 0.13 0.12
Matches are distributed among these distances:
21 46 0.54
22 17 0.20
23 5 0.06
24 11 0.13
25 6 0.07
ACGTcount: A:0.71, C:0.13, G:0.08, T:0.08
Consensus pattern (20 bp):
AAACAACAAAAAAACAGCAA
Found at i:940 original size:24 final size:24
Alignment explanation
Indices: 895--940 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
885 ACAACACCCA
**
895 AACAACAAAAAGAACAGCAAAAAC
1 AACAACAAAAAGAACAAAAAAAAC
* *
919 AACAATAAAAATAACAAAAAAA
1 AACAACAAAAAGAACAAAAAAA
941 TAGTAAAAAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.76, C:0.15, G:0.04, T:0.04
Consensus pattern (24 bp):
AACAACAAAAAGAACAAAAAAAAC
Found at i:970 original size:56 final size:59
Alignment explanation
Indices: 901--1010 Score: 163
Period size: 56 Copynumber: 1.9 Consensus size: 59
891 CCCAAACAAC
* *
901 AAAAAGAACAGCAAAAACAACAATAAAAATAACAAAAA-AATAGTAAAAATAACTGGAA
1 AAAAAGAACAGCAAAAACAACAATAAAAACAACAAAAACAACAGTAAAAATAACTGGAA
* *
959 AAAAAG-A-AGCAAAAATAACAGTAAAAACAACAAAAACAACAGTAAAAATAAC
1 AAAAAGAACAGCAAAAACAACAATAAAAACAACAAAAACAACAGTAAAAATAAC
1011 AACAAAAACA
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
56 26 0.55
57 15 0.32
58 6 0.13
ACGTcount: A:0.71, C:0.12, G:0.08, T:0.09
Consensus pattern (59 bp):
AAAAAGAACAGCAAAAACAACAATAAAAACAACAAAAACAACAGTAAAAATAACTGGAA
Found at i:984 original size:12 final size:12
Alignment explanation
Indices: 901--1011 Score: 58
Period size: 12 Copynumber: 9.8 Consensus size: 12
891 CCCAAACAAC
* *
901 AAAAAGAACAGC
1 AAAAATAACAGT
* *
913 AAAAACAACAAT
1 AAAAATAACAGT
925 AAAAATAAC---
1 AAAAATAACAGT
*
934 AAAAA-AATAGT
1 AAAAATAACAGT
* *
945 AAAAATAACTGG
1 AAAAATAACAGT
* *
957 AAAAA-AAGAAGC
1 AAAAATAA-CAGT
969 AAAAATAACAGT
1 AAAAATAACAGT
*
981 AAAAACAAC---
1 AAAAATAACAGT
*
990 AAAAACAACAGT
1 AAAAATAACAGT
1002 AAAAATAACA
1 AAAAATAACA
1012 ACAAAAACAG
Statistics
Matches: 75, Mismatches: 15, Indels: 18
0.69 0.14 0.17
Matches are distributed among these distances:
8 2 0.03
9 14 0.19
11 7 0.09
12 50 0.67
13 2 0.03
ACGTcount: A:0.71, C:0.12, G:0.08, T:0.09
Consensus pattern (12 bp):
AAAAATAACAGT
Found at i:1022 original size:21 final size:21
Alignment explanation
Indices: 959--1023 Score: 78
Period size: 21 Copynumber: 3.0 Consensus size: 21
949 ATAACTGGAA
* *
959 AAAAAGAAGCAAAAATAACAGT
1 AAAAACAA-CAAAAACAACAGT
981 AAAAACAACAAAAACAACAGT
1 AAAAACAACAAAAACAACAGT
*
1002 AAAAATAACAACAAA-AACAGT
1 AAAAACAACAA-AAACAACAGT
1023 A
1 A
1024 TACTAACAAC
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
21 29 0.74
22 10 0.26
ACGTcount: A:0.71, C:0.14, G:0.08, T:0.08
Consensus pattern (21 bp):
AAAAACAACAAAAACAACAGT
Found at i:1769 original size:30 final size:31
Alignment explanation
Indices: 1733--1799 Score: 100
Period size: 30 Copynumber: 2.2 Consensus size: 31
1723 TTTGGTGTTC
**
1733 AAACTTGACACGTTTTCTTAATTTGGTAC-T
1 AAACTTGACACGTTTTCTTAACCTGGTACTT
*
1763 AAACTTGACACTTTTTCTTAACCTGGTACTT
1 AAACTTGACACGTTTTCTTAACCTGGTACTT
1794 AAACTT
1 AAACTT
1800 TTTGAGGTCC
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
30 26 0.79
31 7 0.21
ACGTcount: A:0.28, C:0.19, G:0.10, T:0.42
Consensus pattern (31 bp):
AAACTTGACACGTTTTCTTAACCTGGTACTT
Done.