Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001311.1 Kokia drynarioides strain JFW-HI SEQ_112727, 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: 27959
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.35
Found at i:2435 original size:2 final size:2
Alignment explanation
Indices: 2428--2463 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2418 AAATTATTCA
2428 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2464 TGAAATTAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4241 original size:72 final size:72
Alignment explanation
Indices: 4108--4247 Score: 174
Period size: 72 Copynumber: 1.9 Consensus size: 72
4098 CTTCAAGAGA
* * *
4108 CACACGGGCGTGTGCCAGACCATGTGTACATACTGTTTTGTAAAATACATTACAGAAGACACATG
1 CACACGGGCGTGTGCCAAACCATGTGTACATACTGTTTTGTAAAATACAGTACAGAAGACACACG
4173 GGCTGGG
66 GGCTGGG
* * * * * **
4180 CACACGGGCGTGTGTCAAACCGTGTGTGCATACTGTTTTGTGAATTA-AGGTACAGGGGACACAC
1 CACACGGGCGTGTGCCAAACCATGTGTACATACTGTTTTGTAAAATACA-GTACAGAAGACACAC
4244 GGGC
65 GGGC
4248 GTGTGGCAGG
Statistics
Matches: 57, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
71 1 0.02
72 56 0.98
ACGTcount: A:0.26, C:0.21, G:0.29, T:0.24
Consensus pattern (72 bp):
CACACGGGCGTGTGCCAAACCATGTGTACATACTGTTTTGTAAAATACAGTACAGAAGACACACG
GGCTGGG
Found at i:5381 original size:3 final size:3
Alignment explanation
Indices: 5375--5407 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
5365 ATAATAATAT
5375 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
5408 AACCACAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:8240 original size:4 final size:4
Alignment explanation
Indices: 8231--8255 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
8221 TTGCAGGACC
8231 TACA TACA TACA TACA TACA TACA T
1 TACA TACA TACA TACA TACA TACA T
8256 GAAGTTTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.48, C:0.24, G:0.00, T:0.28
Consensus pattern (4 bp):
TACA
Found at i:8269 original size:101 final size:101
Alignment explanation
Indices: 8141--8617 Score: 685
Period size: 101 Copynumber: 4.7 Consensus size: 101
8131 TTCTTGCAGG
* * * ** *
8141 TACATACATACATAGAAGTTTTAAGCTTTGGTTGTATGAGCCAGAGGCATTAAATGTGAAGCTAA
1 TACATACATACAT-GAAGTTTTAAGCTTTGATTGTATGAGCTAGGGGCAAAAAATTTGAAGCTAA
*
8206 AACCATGGGAAAATCTTGCAGGACCTACATACATACA
65 AACCATGGGAAAATCTTGCAGGACCTGCATACATACA
* * *
8243 TACATACATACATGAAGTTTTAAGCTTTGATTGTATGAGCTAGGGGCCAAAACTCTGAAGCTAAA
1 TACATACATACATGAAGTTTTAAGCTTTGATTGTATGAGCTAGGGGCAAAAAATTTGAAGCTAAA
*
8308 AGCATGGGAAAATCTTGCAGGACCTG----CATACA
66 ACCATGGGAAAATCTTGCAGGACCTGCATACATACA
*
8340 TACATGCATACATGAAGTTTTAAGCTTTGATTGTATGAGCTAGGGGCAAAAAATTTGAAGCTAAA
1 TACATACATACATGAAGTTTTAAGCTTTGATTGTATGAGCTAGGGGCAAAAAATTTGAAGCTAAA
*
8405 ACCATGGGAAAATCTTGCAGGACCTGCATATGCA-AGA
66 ACCATGGGAAAATCTTGCAGGACCTGCATA--CATACA
* * * *
8442 TCTACATACATACATCAAGTCTTAAGCTTTAATTGTATGAGCGAGGGGCAAAAAATTTGAAGCTA
1 --TACATACATACATGAAGTTTTAAGCTTTGATTGTATGAGCTAGGGGCAAAAAATTTGAAGCTA
*
8507 AAACCATGGGAAAATCTAGCAGGACCTGCATACATACA
64 AAACCATGGGAAAATCTTGCAGGACCTGCATACATACA
* **
8545 TACATACATACATGAAGTTTTAAGCTTTGATTGTATGAGCTAGGGGCCAAATTTTTGAAGCTAAA
1 TACATACATACATGAAGTTTTAAGCTTTGATTGTATGAGCTAGGGGCAAAAAATTTGAAGCTAAA
8610 ACCATGGG
66 ACCATGGG
8618 GGGTTTATGT
Statistics
Matches: 336, Mismatches: 30, Indels: 19
0.87 0.08 0.05
Matches are distributed among these distances:
97 92 0.27
101 134 0.40
102 17 0.05
103 4 0.01
104 89 0.26
ACGTcount: A:0.36, C:0.16, G:0.21, T:0.27
Consensus pattern (101 bp):
TACATACATACATGAAGTTTTAAGCTTTGATTGTATGAGCTAGGGGCAAAAAATTTGAAGCTAAA
ACCATGGGAAAATCTTGCAGGACCTGCATACATACA
Found at i:9459 original size:5 final size:5
Alignment explanation
Indices: 9455--9485 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
9445 TTGAAATGGA
*
9455 GTGGA GTGGG GTGGG GTGGG GTGGG GTGGG G
1 GTGGG GTGGG GTGGG GTGGG GTGGG GTGGG G
9486 CATAGTGGGG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.03, C:0.00, G:0.77, T:0.19
Consensus pattern (5 bp):
GTGGG
Found at i:10216 original size:13 final size:13
Alignment explanation
Indices: 10198--10222 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
10188 AAAATTAATT
10198 TTTTTTTTTTTTA
1 TTTTTTTTTTTTA
10211 TTTTTTTTTTTT
1 TTTTTTTTTTTT
10223 GAATTCAGGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.04, C:0.00, G:0.00, T:0.96
Consensus pattern (13 bp):
TTTTTTTTTTTTA
Found at i:25934 original size:18 final size:18
Alignment explanation
Indices: 25907--25951 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 18
25897 AATAAATGAT
25907 TTAA-AATAATAGCAAAA-
1 TTAATAATAATA-CAAAAG
25924 TTAATAATAATACAAAAG
1 TTAATAATAATACAAAAG
25942 TTATATAATA
1 TTA-ATAATA
25952 TCTAAATAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
17 9 0.36
18 10 0.40
19 6 0.24
ACGTcount: A:0.60, C:0.04, G:0.04, T:0.31
Consensus pattern (18 bp):
TTAATAATAATACAAAAG
Found at i:26817 original size:13 final size:14
Alignment explanation
Indices: 26794--26823 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
26784 TAGGTTTAAA
26794 AAATTTAATTAATT
1 AAATTTAATTAATT
26808 AAATTT-ATTAATT
1 AAATTTAATTAATT
26821 AAA
1 AAA
26824 AATTTATTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.62
14 6 0.38
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
AAATTTAATTAATT
Found at i:26828 original size:15 final size:15
Alignment explanation
Indices: 26792--26831 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
26782 TTTAGGTTTA
26792 AAAAATTTAATTAATT
1 AAAAATTT-ATTAATT
26808 --AAATTTATTAATT
1 AAAAATTTATTAATT
26821 AAAAATTTATT
1 AAAAATTTATT
26832 CTCATCCCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
13 7 0.32
14 6 0.27
15 9 0.41
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
AAAAATTTATTAATT
Found at i:27833 original size:4 final size:4
Alignment explanation
Indices: 27824--27890 Score: 64
Period size: 4 Copynumber: 16.2 Consensus size: 4
27814 AAATAAACGG
* *
27824 GAAA GAAA GAAA GAAAA GAAA GAAA GAAA GAAA GGAAG GAGAG GAAA GAAA
1 GAAA GAAA GAAA G-AAA GAAA GAAA GAAA GAAA -GAAA GA-AA GAAA GAAA
* *
27875 -TAA GAAG GAAA GAAA G
1 GAAA GAAA GAAA GAAA G
27891 GTAATGTATT
Statistics
Matches: 53, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
3 2 0.04
4 40 0.75
5 11 0.21
ACGTcount: A:0.67, C:0.00, G:0.31, T:0.01
Consensus pattern (4 bp):
GAAA
Found at i:27846 original size:17 final size:17
Alignment explanation
Indices: 27824--27890 Score: 71
Period size: 17 Copynumber: 3.8 Consensus size: 17
27814 AAATAAACGG
27824 GAAAGAAAGAAAGAAAA
1 GAAAGAAAGAAAGAAAA
*
27841 GAAAGAAAGAAAGAAAG
1 GAAAGAAAGAAAGAAAA
* *
27858 GAAGGAGAGGAAAGAAATAA
1 GAAAGA-AAGAAAG-AA-AA
*
27878 GAAGGAAAGAAAG
1 GAAAGAAAGAAAG
27891 GTAATGTATT
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
17 21 0.50
18 6 0.14
19 8 0.19
20 7 0.17
ACGTcount: A:0.67, C:0.00, G:0.31, T:0.01
Consensus pattern (17 bp):
GAAAGAAAGAAAGAAAA
Done.