Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002540.1 Kokia drynarioides strain JFW-HI SEQ_114721, 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: 24907
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.32
Found at i:2940 original size:14 final size:14
Alignment explanation
Indices: 2923--2958 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
2913 TCTCAAATTG
*
2923 AAAAAGATAAAGAA
1 AAAAAGATAAAAAA
*
2937 AAAAAGAAAAAAAA
1 AAAAAGATAAAAAA
2951 AAAAAGAT
1 AAAAAGAT
2959 TACTAAGTAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.83, C:0.00, G:0.11, T:0.06
Consensus pattern (14 bp):
AAAAAGATAAAAAA
Found at i:15608 original size:29 final size:30
Alignment explanation
Indices: 15535--15614 Score: 76
Period size: 29 Copynumber: 2.7 Consensus size: 30
15525 TAGGGTAAAC
* *
15535 TACACTAATTATCCCTAAACTTTGATTAAAAT
1 TACA-TAATTATCACTAAACTTTCA-TAAAAT
* *
15567 TACAT-TTTGATCACTTAACTTTCA-AAAAT
1 TACATAATT-ATCACTAAACTTTCATAAAAT
15596 TACATAATTATCA-TAAACT
1 TACATAATTATCACTAAACT
15615 GTTACATTTT
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
28 5 0.12
29 14 0.35
30 4 0.10
31 13 0.32
32 4 0.10
ACGTcount: A:0.41, C:0.17, G:0.03, T:0.39
Consensus pattern (30 bp):
TACATAATTATCACTAAACTTTCATAAAAT
Found at i:16679 original size:22 final size:22
Alignment explanation
Indices: 16645--16686 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
16635 GTGTGAGATG
16645 AAAAAGAGAGTTGAAAGTGAAA
1 AAAAAGAGAGTTGAAAGTGAAA
* * *
16667 AAAAATAGTGTTGCAAGTGA
1 AAAAAGAGAGTTGAAAGTGA
16687 GAAGCAAAAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.52, C:0.02, G:0.26, T:0.19
Consensus pattern (22 bp):
AAAAAGAGAGTTGAAAGTGAAA
Found at i:21239 original size:21 final size:21
Alignment explanation
Indices: 21215--21264 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
21205 TGTGTGAGCT
* *
21215 AAAAAAGAGAGTTGTAAGTGA
1 AAAAAACAGAGCTGTAAGTGA
*
21236 AAAAAACAGTGCTGTAAGTGA
1 AAAAAACAGAGCTGTAAGTGA
21257 AACAAAAC
1 AA-AAAAC
21265 TAGCAGCAGC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
21 20 0.80
22 5 0.20
ACGTcount: A:0.54, C:0.08, G:0.22, T:0.16
Consensus pattern (21 bp):
AAAAAACAGAGCTGTAAGTGA
Found at i:21807 original size:21 final size:22
Alignment explanation
Indices: 21782--21844 Score: 67
Period size: 20 Copynumber: 2.9 Consensus size: 22
21772 AACAATAGTA
*
21782 AAAATGCATAAAAATAACATCC
1 AAAATGCATAAAAATAACAACC
*
21804 -AAAT-AATAAAAATAACAACC
1 AAAATGCATAAAAATAACAACC
*
21824 AAAATAGCAACAAAAATAACA
1 AAAAT-GC-ATAAAAATAACA
21845 GCAAAACGAC
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
20 14 0.42
21 8 0.24
24 11 0.33
ACGTcount: A:0.67, C:0.16, G:0.03, T:0.14
Consensus pattern (22 bp):
AAAATGCATAAAAATAACAACC
Found at i:21829 original size:12 final size:12
Alignment explanation
Indices: 21811--21924 Score: 76
Period size: 12 Copynumber: 9.8 Consensus size: 12
21801 TCCAAATAAT
21811 AAAAATAACAAC
1 AAAAATAACAAC
* *
21823 CAAAATAGCAAC
1 AAAAATAACAAC
*
21835 AAAAATAACAGC
1 AAAAATAACAAC
*
21847 ---AA-AACGAC
1 AAAAATAACAAC
*
21855 AACAA-AACAAC
1 AAAAATAACAAC
* *
21866 AAAAATAGCTAC
1 AAAAATAACAAC
**
21878 AAAAATCGCAAC
1 AAAAATAACAAC
*
21890 AAAAATAACAAAA
1 AAAAATAAC-AAC
*
21903 AAAAATAGCAAC
1 AAAAATAACAAC
*
21915 AAAGATAACA
1 AAAAATAACA
21925 GCATCAAAAC
Statistics
Matches: 77, Mismatches: 20, Indels: 10
0.72 0.19 0.09
Matches are distributed among these distances:
8 4 0.05
9 2 0.03
11 11 0.14
12 50 0.65
13 10 0.13
ACGTcount: A:0.68, C:0.18, G:0.06, T:0.08
Consensus pattern (12 bp):
AAAAATAACAAC
Found at i:21871 original size:43 final size:39
Alignment explanation
Indices: 21817--21927 Score: 109
Period size: 43 Copynumber: 2.8 Consensus size: 39
21807 TAATAAAAAT
*
21817 AACAACCAAAATAGCAACAAAAATAACAGCAAAACGACAAC
1 AACAACAAAAATAGCAACAAAAATAACAGCAAAA--ACAAC
* ** * *
21858 AAAACAACAAAAATAGCTACAAAAATCGCAACAAAAATAAC
1 --AACAACAAAAATAGCAACAAAAATAACAGCAAAAACAAC
*
21899 AA-AA-AAAAATAGCAACAAAGATAACAGCA
1 AACAACAAAAATAGCAACAAAAATAACAGCA
21928 TCAAAACAGT
Statistics
Matches: 57, Mismatches: 11, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
37 20 0.35
38 2 0.04
39 2 0.04
41 4 0.07
43 29 0.51
ACGTcount: A:0.66, C:0.20, G:0.07, T:0.07
Consensus pattern (39 bp):
AACAACAAAAATAGCAACAAAAATAACAGCAAAAACAAC
Found at i:21881 original size:31 final size:33
Alignment explanation
Indices: 21831--21903 Score: 82
Period size: 33 Copynumber: 2.3 Consensus size: 33
21821 ACCAAAATAG
21831 CAACAAAAATAACAGC-AAAA-CGACAAC-AAAA
1 CAACAAAAATAACAGCAAAAATCG-CAACAAAAA
*
21862 CAACAAAAATAGCTA-CAAAAATCGCAACAAAAA
1 CAACAAAAATAAC-AGCAAAAATCGCAACAAAAA
*
21895 TAACAAAAA
1 CAACAAAAA
21904 AAAATAGCAA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
31 13 0.36
32 9 0.25
33 14 0.39
ACGTcount: A:0.67, C:0.21, G:0.05, T:0.07
Consensus pattern (33 bp):
CAACAAAAATAACAGCAAAAATCGCAACAAAAA
Found at i:21948 original size:21 final size:20
Alignment explanation
Indices: 21929--22023 Score: 72
Period size: 21 Copynumber: 4.8 Consensus size: 20
21919 ATAACAGCAT
21929 CAAAACAGTAAAAAAAAGCAC
1 CAAAACAGTAAAAAAAA-CAC
* *
21950 CGAAATAGT---AAAAA-AC
1 CAAAACAGTAAAAAAAACAC
* * *
21966 TAAAATAGTAGAAAACAACAC
1 CAAAACAGTA-AAAAAAACAC
21987 CAAAACAGTAAAAAACAACAAC
1 CAAAACAGTAAAAAA-AAC-AC
*
22009 CAAAACAATAAAAAA
1 CAAAACAGTAAAAAA
22024 TAGCACAAAA
Statistics
Matches: 58, Mismatches: 9, Indels: 13
0.73 0.11 0.16
Matches are distributed among these distances:
16 9 0.16
18 5 0.09
20 8 0.14
21 20 0.34
22 16 0.28
ACGTcount: A:0.67, C:0.17, G:0.07, T:0.08
Consensus pattern (20 bp):
CAAAACAGTAAAAAAAACAC
Found at i:22013 original size:22 final size:21
Alignment explanation
Indices: 21967--22023 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
21957 GTAAAAAACT
* *
21967 AAAATAGTAGAAAACAACACC
1 AAAACAGTAAAAAACAACACC
21988 AAAACAGTAAAAAACAACAACC
1 AAAACAGTAAAAAACAAC-ACC
*
22010 AAAACAATAAAAAA
1 AAAACAGTAAAAAA
22024 TAGCACAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
21 16 0.50
22 16 0.50
ACGTcount: A:0.70, C:0.18, G:0.05, T:0.07
Consensus pattern (21 bp):
AAAACAGTAAAAAACAACACC
Done.