Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003390.1 Kokia drynarioides strain JFW-HI SEQ_116128, 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: 41705
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34
Found at i:953 original size:17 final size:17
Alignment explanation
Indices: 931--967 Score: 53
Period size: 14 Copynumber: 2.4 Consensus size: 17
921 ACAGTTGCAG
931 TGAAGTAGTGATAGTAT
1 TGAAGTAGTGATAGTAT
948 TG-A--AGTGATAGTAT
1 TGAAGTAGTGATAGTAT
962 TGAAGT
1 TGAAGT
968 GTAGATGGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 6
0.74 0.00 0.26
Matches are distributed among these distances:
14 13 0.76
15 1 0.06
16 1 0.06
17 2 0.12
ACGTcount: A:0.35, C:0.00, G:0.30, T:0.35
Consensus pattern (17 bp):
TGAAGTAGTGATAGTAT
Found at i:956 original size:14 final size:14
Alignment explanation
Indices: 937--968 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
927 GCAGTGAAGT
937 AGTGATAGTATTGA
1 AGTGATAGTATTGA
951 AGTGATAGTATTGA
1 AGTGATAGTATTGA
965 AGTG
1 AGTG
969 TAGATGGATC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.34, C:0.00, G:0.31, T:0.34
Consensus pattern (14 bp):
AGTGATAGTATTGA
Found at i:3775 original size:15 final size:16
Alignment explanation
Indices: 3754--3798 Score: 58
Period size: 15 Copynumber: 2.8 Consensus size: 16
3744 ATTTTGATAA
3754 AAATAAAATTAAAAAT
1 AAATAAAATTAAAAAT
3770 -AAT-AAATTAAAAAAT
1 AAATAAAATT-AAAAAT
3785 AAATAAAATATAAA
1 AAATAAAAT-TAAA
3799 GTATTTAGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
14 5 0.20
15 9 0.36
16 3 0.12
17 7 0.28
18 1 0.04
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (16 bp):
AAATAAAATTAAAAAT
Found at i:3788 original size:12 final size:12
Alignment explanation
Indices: 3752--3798 Score: 51
Period size: 11 Copynumber: 3.8 Consensus size: 12
3742 AAATTTTGAT
3752 AAAAATAAAATTAA
1 AAAAAT-AAATT-A
3766 AAATAATAAATTA
1 AAA-AATAAATTA
3779 AAAAATAAA-TA
1 AAAAATAAATTA
*
3790 AAATATAAA
1 AAAAATAAA
3799 GTATTTAGAA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
11 10 0.32
12 6 0.19
13 4 0.13
14 8 0.26
15 3 0.10
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (12 bp):
AAAAATAAATTA
Found at i:5141 original size:30 final size:30
Alignment explanation
Indices: 5105--5164 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
5095 TTAGTTTCAA
*
5105 AATAGAAA-ATAATTCATTCAAAAATTAAAT
1 AATAGAAATA-AATTAATTCAAAAATTAAAT
* *
5135 AATAGAATTAAATTAATTCTAAAATTAAAT
1 AATAGAAATAAATTAATTCAAAAATTAAAT
5165 GAAAATATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 25 0.96
31 1 0.04
ACGTcount: A:0.58, C:0.05, G:0.03, T:0.33
Consensus pattern (30 bp):
AATAGAAATAAATTAATTCAAAAATTAAAT
Found at i:5625 original size:19 final size:19
Alignment explanation
Indices: 5601--5653 Score: 72
Period size: 19 Copynumber: 2.7 Consensus size: 19
5591 AAATTTTTTA
5601 TCTATAAAATTATTAAT-TT
1 TCTATAAAA-TATTAATATT
5620 TCTATAAAACTATTAATATT
1 TCTATAAAA-TATTAATATT
*
5640 TCAATAAAATATTA
1 TCTATAAAATATTA
5654 CACCATCGGT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
19 21 0.68
20 10 0.32
ACGTcount: A:0.47, C:0.08, G:0.00, T:0.45
Consensus pattern (19 bp):
TCTATAAAATATTAATATT
Found at i:5884 original size:15 final size:14
Alignment explanation
Indices: 5859--5888 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
5849 CTCGGCTGCA
5859 ACACCAACCAAACC
1 ACACCAACCAAACC
5873 ACACCAAACCAAACC
1 ACACC-AACCAAACC
5888 A
1 A
5889 AAAGCCACCC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.53, C:0.47, G:0.00, T:0.00
Consensus pattern (14 bp):
ACACCAACCAAACC
Found at i:6691 original size:2 final size:2
Alignment explanation
Indices: 6684--6710 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
6674 GGTTGATTCT
6684 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
6711 TCATTACGTG
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:18906 original size:2 final size:2
Alignment explanation
Indices: 18899--18929 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
18889 AATCAAGGTA
*
18899 AC AC AC AC AC AC AC AC AT AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
18930 TATATATATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.45, G:0.00, T:0.03
Consensus pattern (2 bp):
AC
Found at i:36806 original size:25 final size:25
Alignment explanation
Indices: 36778--36827 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
36768 TACATATTAT
*
36778 ATATACAAAT-AATTATATTTATTTA
1 ATATACAAATGAATTA-ATATATTTA
*
36803 ATATAGAAATGAATTAATATATTTA
1 ATATACAAATGAATTAATATATTTA
36828 TTTATTAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 17 0.77
26 5 0.23
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.44
Consensus pattern (25 bp):
ATATACAAATGAATTAATATATTTA
Found at i:40037 original size:2 final size:2
Alignment explanation
Indices: 40030--40064 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
40020 TGCACCTCCC
40030 TA TA TA TA 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 TA TA TA TA T
40065 TTCTTCTTCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Done.