Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014537.1 Kokia drynarioides strain JFW-HI SEQ_129576, 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: 48573
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Found at i:4358 original size:3 final size:3
Alignment explanation
Indices: 4350--4386 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
4340 ATTCAGTCCG
4350 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
4387 TTAAATGTCC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:6884 original size:91 final size:87
Alignment explanation
Indices: 6722--6904 Score: 237
Period size: 91 Copynumber: 2.1 Consensus size: 87
6712 GCCTTTTTTG
*
6722 TTTTTAGTTTAAAAGTAATAGTTCTGTTCTTGAATTAAATCGTATTATTTTTGTGTAATTTTTTA
1 TTTTTAGTTTAAAAGTAATAGTTCTGTTCTTGAATTAAATCGTATTATTTTTGTGTAATTTCTTA
6787 GCAATCCGACTGGAT-CGT-CT
66 GCAATCCGACTGGATCCGTACT
* * *
6807 TTTTTAAGTTTTAAATTAATAGTT-TGTTCTTGAATTGAATCGTATTTCTGGTATTTTTGTGTAA
1 TTTTT-AGTTTAAAAGTAATAGTTCTGTTCTTGAATTAAATCGTA----T--TATTTTTGTGTAA
*
6871 TTTCTTAGTAATCCGACTGGATCCGTACT
59 TTTCTTAGCAATCCGACTGGATCCGTACT
6900 TTTTT
1 TTTTT
6905 TTCTGTTGAT
Statistics
Matches: 84, Mismatches: 5, Indels: 10
0.85 0.05 0.10
Matches are distributed among these distances:
85 24 0.29
86 16 0.19
89 1 0.01
91 33 0.39
92 3 0.04
93 7 0.08
ACGTcount: A:0.24, C:0.10, G:0.15, T:0.50
Consensus pattern (87 bp):
TTTTTAGTTTAAAAGTAATAGTTCTGTTCTTGAATTAAATCGTATTATTTTTGTGTAATTTCTTA
GCAATCCGACTGGATCCGTACT
Found at i:6945 original size:108 final size:108
Alignment explanation
Indices: 6806--7001 Score: 311
Period size: 108 Copynumber: 1.8 Consensus size: 108
6796 CTGGATCGTC
* * * * *
6806 TTTTTTAAGTTTTAAATTAATAGTTTGTTCTTGAATTGAATCGTATTTCTGGTATTTTTGTGTAA
1 TTTTTTAAGTTTTAAATTAATAGGTTATTCTTGAATTGAATCGTATTTCAGATATATTTGTGTAA
*
6871 TTTCTTAGTAATCCGACTGGATCCGTACTTTTTTTTCTGTTGA
66 TTTCTTAGCAATCCGACTGGATCCGTACTTTTTTTTCTGTTGA
* * *
6914 TTTTTTAAGTTTTAAATTAGTAGGTTATTCTTGAATTTAATCGTATTTCAGATATATTTGTGTGA
1 TTTTTTAAGTTTTAAATTAATAGGTTATTCTTGAATTGAATCGTATTTCAGATATATTTGTGTAA
6979 TTTCTTAGCAATCCGACTGGATC
66 TTTCTTAGCAATCCGACTGGATC
7002 GTCATTGAAC
Statistics
Matches: 79, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
108 79 1.00
ACGTcount: A:0.23, C:0.10, G:0.16, T:0.51
Consensus pattern (108 bp):
TTTTTTAAGTTTTAAATTAATAGGTTATTCTTGAATTGAATCGTATTTCAGATATATTTGTGTAA
TTTCTTAGCAATCCGACTGGATCCGTACTTTTTTTTCTGTTGA
Found at i:10764 original size:95 final size:94
Alignment explanation
Indices: 10517--10765 Score: 249
Period size: 95 Copynumber: 2.6 Consensus size: 94
10507 TTGTTGTTTA
*
10517 GTTTT-TGATTTTTAGTGTAATTTCTTAGCAATCCGACTAGATCTTTACTTTTTTTTTTTTAGTT
1 GTTTTCTGATTTTTAGTGTAATTTCTTAGCAATCCGACT-GATCTTTAC-TTTTTTTTTTAAGTT
* *
10581 TAAAATTAATTGTTTATCCTTGAATTAGATC
64 TAAAATTAATAGTTTAACCTTGAATTAGATC
* * ** * ** **
10612 GTATTTCTGATATTCTT-GTGTAATTTC-GA-CAGGAT-CGTCTTTTTTTTTGTTGATTTTTTAA
1 GT-TTTCTGAT-TT-TTAGTGTAATTTCTTAGCA--ATCCGACTGATCTTTACTTTTTTTTTTAA
* *
10673 GTTTTAAATTAATAGTTTAAGCTTGAATTTA-ATC
61 GTTTAAAATTAATAGTTTAACCTTGAA-TTAGATC
10707 GTTTTCTGATTTTTAGTGTAATTTCTTAGCAATCCGACTGGATCTTTACTTTTTTTTTT
1 GTTTTCTGATTTTTAGTGTAATTTCTTAGCAATCCGACT-GATCTTTACTTTTTTTTTT
10766 TTTTTTATTC
Statistics
Matches: 119, Mismatches: 23, Indels: 24
0.72 0.14 0.14
Matches are distributed among these distances:
92 2 0.02
93 14 0.12
94 13 0.11
95 53 0.45
96 12 0.10
97 9 0.08
98 14 0.12
99 2 0.02
ACGTcount: A:0.22, C:0.10, G:0.13, T:0.54
Consensus pattern (94 bp):
GTTTTCTGATTTTTAGTGTAATTTCTTAGCAATCCGACTGATCTTTACTTTTTTTTTTAAGTTTA
AAATTAATAGTTTAACCTTGAATTAGATC
Found at i:14399 original size:16 final size:16
Alignment explanation
Indices: 14378--14415 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
14368 AATTTAGTTA
*
14378 TTATAGCGAAATG-TTG
1 TTATAGC-AAATGACTG
14394 TTATAGCAAATGACTG
1 TTATAGCAAATGACTG
14410 TTATAG
1 TTATAG
14416 AAGACTATCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 5 0.25
16 15 0.75
ACGTcount: A:0.34, C:0.08, G:0.21, T:0.37
Consensus pattern (16 bp):
TTATAGCAAATGACTG
Found at i:16059 original size:43 final size:43
Alignment explanation
Indices: 15998--16089 Score: 123
Period size: 43 Copynumber: 2.1 Consensus size: 43
15988 CTAACCATAT
* * *
15998 ATTAATTAGTATATGCTTATAATAAACATTGATTT-ATAATAA
1 ATTAATTAGTATAAGCTTACAATAAACAATGATTTGATAATAA
* *
16040 ATTAATTAAGTATAAGCTTACACTAAACAATGATTTGTTAATAA
1 ATTAATT-AGTATAAGCTTACAATAAACAATGATTTGATAATAA
16084 ATTAAT
1 ATTAAT
16090 CCTTAGTCTA
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
42 7 0.16
43 24 0.56
44 12 0.28
ACGTcount: A:0.46, C:0.07, G:0.08, T:0.40
Consensus pattern (43 bp):
ATTAATTAGTATAAGCTTACAATAAACAATGATTTGATAATAA
Found at i:27813 original size:22 final size:22
Alignment explanation
Indices: 27771--27813 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
27761 AAGTGAAACT
*
27771 AAACTTTTAAACTGTTGTTGAC
1 AAACTTTTAAACTATTGTTGAC
*
27793 AAAC-TTTAACCTATTGATTGA
1 AAACTTTTAAACTATTG-TTGA
27814 GGGGCATAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.40
Consensus pattern (22 bp):
AAACTTTTAAACTATTGTTGAC
Found at i:36841 original size:29 final size:29
Alignment explanation
Indices: 36783--36850 Score: 68
Period size: 31 Copynumber: 2.3 Consensus size: 29
36773 ATAAATATCA
* *
36783 AATTTATATATAAATTTTGGTTTGATGTGT
1 AATTTATATATAAACTTTGATTTGA-GTGT
*
36813 AATTTGATATATTAACTTTGATTTG-GTGT
1 AATTT-ATATATAAACTTTGATTTGAGTGT
*
36842 -ACTTATATA
1 AATTTATATA
36851 CATGAAATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
27 5 0.15
28 3 0.09
29 4 0.12
30 5 0.15
31 16 0.48
ACGTcount: A:0.31, C:0.03, G:0.15, T:0.51
Consensus pattern (29 bp):
AATTTATATATAAACTTTGATTTGAGTGT
Found at i:39451 original size:2 final size:2
Alignment explanation
Indices: 39444--39468 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
39434 CGTTGTTGGG
39444 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
39469 ATTAAATTAT
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:40297 original size:15 final size:14
Alignment explanation
Indices: 40256--40300 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
40246 AAATTGTGAA
*
40256 TTTAATTTATATAT
1 TTTAATTTTTATAT
*
40270 TTTAA-TTTGATAT
1 TTTAATTTTTATAT
40283 TATTAATTTTTATAT
1 T-TTAATTTTTATAT
40298 TTT
1 TTT
40301 TTAAATTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
13 7 0.27
14 11 0.42
15 8 0.31
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (14 bp):
TTTAATTTTTATAT
Done.