Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010232.1 Kokia drynarioides strain JFW-HI SEQ_125062, 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: 48571
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:5841 original size:68 final size:68
Alignment explanation
Indices: 5732--5870 Score: 242
Period size: 68 Copynumber: 2.0 Consensus size: 68
5722 ACACATCTAA
* *
5732 TGTTGATAGATTCGGTAGGAGCAAATTGTATCCCATATTAGCATAGCAACCTACCCATGGTTTAC
1 TGTTGATAGATTCGGTAAGAGCAAATTGTATCCCATATTAGCATAGCAACCTACCCATGGCTTAC
5797 CTG
66 CTG
* *
5800 TGTTGGTAGATTCGGTAAGAGCCAATTGTATCCCATATTAGCATAGCAACCTACCCATGGCTTAC
1 TGTTGATAGATTCGGTAAGAGCAAATTGTATCCCATATTAGCATAGCAACCTACCCATGGCTTAC
5865 CTG
66 CTG
5868 TGT
1 TGT
5871 CAACAATTTT
Statistics
Matches: 67, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
68 67 1.00
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.31
Consensus pattern (68 bp):
TGTTGATAGATTCGGTAAGAGCAAATTGTATCCCATATTAGCATAGCAACCTACCCATGGCTTAC
CTG
Found at i:7016 original size:13 final size:13
Alignment explanation
Indices: 6998--7023 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
6988 ACAATGAGCA
6998 AAATAATAATAAT
1 AAATAATAATAAT
7011 AAATAATAATAAT
1 AAATAATAATAAT
7024 TTTATTAACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
AAATAATAATAAT
Found at i:8306 original size:31 final size:31
Alignment explanation
Indices: 8265--8333 Score: 129
Period size: 31 Copynumber: 2.2 Consensus size: 31
8255 GAGTTAAAAA
8265 AGTATGAACAGATATTATCATATAATCACACC
1 AGTAT-AACAGATATTATCATATAATCACACC
8297 AGTATAACAGATATTATCATATAATCACACC
1 AGTATAACAGATATTATCATATAATCACACC
8328 AGTATA
1 AGTATA
8334 TTCAAAAAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 32 0.86
32 5 0.14
ACGTcount: A:0.45, C:0.17, G:0.09, T:0.29
Consensus pattern (31 bp):
AGTATAACAGATATTATCATATAATCACACC
Found at i:8423 original size:60 final size:60
Alignment explanation
Indices: 8330--8444 Score: 221
Period size: 60 Copynumber: 1.9 Consensus size: 60
8320 ATCACACCAG
8330 TATATTCAAAAAAAAAATACTCAATTCGTTTAGGAATCTTGTGTGTTAGCTTGATGATAA
1 TATATTCAAAAAAAAAATACTCAATTCGTTTAGGAATCTTGTGTGTTAGCTTGATGATAA
*
8390 TATATTCAAAAAAAAAATACTCAATTCGTTTAGGAATCTTGTGTGTTGGCTTGAT
1 TATATTCAAAAAAAAAATACTCAATTCGTTTAGGAATCTTGTGTGTTAGCTTGAT
8445 CAAGCGTGTT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 54 1.00
ACGTcount: A:0.37, C:0.10, G:0.16, T:0.37
Consensus pattern (60 bp):
TATATTCAAAAAAAAAATACTCAATTCGTTTAGGAATCTTGTGTGTTAGCTTGATGATAA
Found at i:9691 original size:3 final size:3
Alignment explanation
Indices: 9683--9710 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
9673 CGTTTAACTA
9683 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
9711 TCTAAAGGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:28044 original size:32 final size:33
Alignment explanation
Indices: 27989--28055 Score: 109
Period size: 32 Copynumber: 2.1 Consensus size: 33
27979 AAACAATCAG
* *
27989 ATGCATAACTTTTAGAGTTATCAATTCTATTAT
1 ATGCAAAACTTTTAGAGTTATCAACTCTATTAT
28022 ATGCAAAACTTTT-GAGTTATCAACTCTATTAT
1 ATGCAAAACTTTTAGAGTTATCAACTCTATTAT
28054 AT
1 AT
28056 TCCTTCCGTC
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 20 0.62
33 12 0.38
ACGTcount: A:0.34, C:0.13, G:0.09, T:0.43
Consensus pattern (33 bp):
ATGCAAAACTTTTAGAGTTATCAACTCTATTAT
Found at i:32066 original size:24 final size:25
Alignment explanation
Indices: 32039--32087 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
32029 GAGTTAGTAT
* *
32039 ATAAATTATTTGAAATT-TGGTTAA
1 ATAAATTAGTCGAAATTGTGGTTAA
*
32063 ATAATTTAGTCGAAATTGTGGTTAA
1 ATAAATTAGTCGAAATTGTGGTTAA
32088 TTAAGACTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 14 0.67
25 7 0.33
ACGTcount: A:0.39, C:0.02, G:0.16, T:0.43
Consensus pattern (25 bp):
ATAAATTAGTCGAAATTGTGGTTAA
Found at i:32916 original size:42 final size:42
Alignment explanation
Indices: 32857--32937 Score: 135
Period size: 42 Copynumber: 1.9 Consensus size: 42
32847 GAATTTATAC
* * *
32857 TTCGGTTTAGCCTATGATGCACTTATGTGCTAGTCTATTTAT
1 TTCGGTTTAACCAATGATGCACTTATGTGCTAGTATATTTAT
32899 TTCGGTTTAACCAATGATGCACTTATGTGCTAGTATATT
1 TTCGGTTTAACCAATGATGCACTTATGTGCTAGTATATT
32938 AACTCCAGTT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.22, C:0.16, G:0.19, T:0.43
Consensus pattern (42 bp):
TTCGGTTTAACCAATGATGCACTTATGTGCTAGTATATTTAT
Found at i:32958 original size:42 final size:42
Alignment explanation
Indices: 32861--32950 Score: 117
Period size: 42 Copynumber: 2.1 Consensus size: 42
32851 TTATACTTCG
* * * * * *
32861 GTTTAGCCTATGATGCACTTATGTGCTAGTCTATTTATTTCG
1 GTTTAGCCAATGATGCACTTATGTGCTAGTATATTAACTCCA
*
32903 GTTTAACCAATGATGCACTTATGTGCTAGTATATTAACTCCA
1 GTTTAGCCAATGATGCACTTATGTGCTAGTATATTAACTCCA
32945 GTTTAG
1 GTTTAG
32951 TCGATGATAT
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.24, C:0.17, G:0.18, T:0.41
Consensus pattern (42 bp):
GTTTAGCCAATGATGCACTTATGTGCTAGTATATTAACTCCA
Found at i:36173 original size:20 final size:20
Alignment explanation
Indices: 36148--36188 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
36138 TCATGGTAAA
36148 TAAATTAGCAGCTAATATGC
1 TAAATTAGCAGCTAATATGC
36168 TAAATTAGCAGCTAATATGC
1 TAAATTAGCAGCTAATATGC
36188 T
1 T
36189 TTATTTTCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.32
Consensus pattern (20 bp):
TAAATTAGCAGCTAATATGC
Found at i:39010 original size:19 final size:19
Alignment explanation
Indices: 38970--39014 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
38960 TTTTATTAGG
38970 ATTTAATATTTAAGATATT
1 ATTTAATATTTAAGATATT
* *
38989 ATTTATTATTTAA-ATTTGT
1 ATTTAATATTTAAGATAT-T
39008 ATTTAAT
1 ATTTAAT
39015 TTATGTTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 3 0.14
19 19 0.86
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (19 bp):
ATTTAATATTTAAGATATT
Found at i:42595 original size:17 final size:18
Alignment explanation
Indices: 42555--42592 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
42545 AAGACAAGAT
*
42555 TAATTGTAATATTTTTTA
1 TAATTATAATATTTTTTA
*
42573 TAATTATAATTTTTTTTA
1 TAATTATAATATTTTTTA
42591 TA
1 TA
42593 TTAGCATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (18 bp):
TAATTATAATATTTTTTA
Found at i:43805 original size:139 final size:139
Alignment explanation
Indices: 43638--43900 Score: 427
Period size: 139 Copynumber: 1.9 Consensus size: 139
43628 CTTTTTCTGT
43638 TTTTCTTTTAAAAAACACTCTTACTTAGATTCACCTTTCTCATCAACAACACGATGGAGCAAACA
1 TTTTCTTTTAAAAAACACTCTTACTTAGATTCACCTTTCTCATCAACAACACGATGGAGCAAACA
* * * * *
43703 AAGTGCTGCTGACGTACTTAGTAATTCCAAGTAGTGGAGTTGAAGTTTTTTCATCTTTTTCCGTT
66 AAATGCTACTGACGTACTCAGTAATTCCAAGCAGTGGAGTGGAAGTTTTTTCATCTTTTTCCGTT
43768 TTTCTTTTA
131 TTTCTTTTA
* *
43777 TTTTCTTTTACAAAATACTCTTACTTAGATTCACCTTTCTCATCAACAACACGATGGAGCAAACA
1 TTTTCTTTTAAAAAACACTCTTACTTAGATTCACCTTTCTCATCAACAACACGATGGAGCAAACA
* * * *
43842 AAATGCTACTGACGTACTCAGTAATTCCAAGCATTGGAGTGGCATTTTTTTCTTCTTTT
66 AAATGCTACTGACGTACTCAGTAATTCCAAGCAGTGGAGTGGAAGTTTTTTCATCTTTT
43901 ATTTGTATTT
Statistics
Matches: 113, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
139 113 1.00
ACGTcount: A:0.28, C:0.21, G:0.13, T:0.38
Consensus pattern (139 bp):
TTTTCTTTTAAAAAACACTCTTACTTAGATTCACCTTTCTCATCAACAACACGATGGAGCAAACA
AAATGCTACTGACGTACTCAGTAATTCCAAGCAGTGGAGTGGAAGTTTTTTCATCTTTTTCCGTT
TTTCTTTTA
Done.