Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004029.1 Kokia drynarioides strain JFW-HI SEQ_117156, 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: 50366
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Warning! 42 characters in sequence are not A, C, G, or T
Found at i:5321 original size:3 final size:3
Alignment explanation
Indices: 5315--5349 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
5305 GCAGCTACTG
* *
5315 CAA CAA CAA CAA CAA CAA CAG CAA CAG CAA CAA CA
1 CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CA
5350 GCGGCAGCAG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.60, C:0.34, G:0.06, T:0.00
Consensus pattern (3 bp):
CAA
Found at i:5350 original size:9 final size:9
Alignment explanation
Indices: 5314--5373 Score: 50
Period size: 9 Copynumber: 6.7 Consensus size: 9
5304 AGCAGCTACT
5314 GCAACAACA
1 GCAACAACA
*
5323 ACAACAACA
1 GCAACAACA
* *
5332 ACAGCAACA
1 GCAACAACA
5341 GCAACAACA
1 GCAACAACA
** *
5350 GCGGCAGCA
1 GCAACAACA
5359 GCAAGCAA-A
1 GCAA-CAACA
5368 GCAACA
1 GCAACA
5374 GCTGTCCACT
Statistics
Matches: 40, Mismatches: 10, Indels: 3
0.75 0.19 0.06
Matches are distributed among these distances:
8 2 0.05
9 36 0.90
10 2 0.05
ACGTcount: A:0.52, C:0.32, G:0.17, T:0.00
Consensus pattern (9 bp):
GCAACAACA
Found at i:9903 original size:14 final size:13
Alignment explanation
Indices: 9885--9909 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
9875 AAAATATATT
9885 TTTTTTTTGTCGA
1 TTTTTTTTGTCGA
9898 TTTTTTTTGTCG
1 TTTTTTTTGTCG
9910 TCATCAATAG
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:0.08, G:0.16, T:0.72
Consensus pattern (13 bp):
TTTTTTTTGTCGA
Found at i:15139 original size:57 final size:57
Alignment explanation
Indices: 15051--15166 Score: 223
Period size: 57 Copynumber: 2.0 Consensus size: 57
15041 TCTTGCCTGG
15051 TTATGTTGGTATTAAACTGTTGGTTGATCAGTTTCATTTTGTATTTTCTACAAGCAA
1 TTATGTTGGTATTAAACTGTTGGTTGATCAGTTTCATTTTGTATTTTCTACAAGCAA
*
15108 TTATGTTGGTATTAAACTGTTGGTTGATCAGTTTCATTTTGTGTTTTCTACAAGCAA
1 TTATGTTGGTATTAAACTGTTGGTTGATCAGTTTCATTTTGTATTTTCTACAAGCAA
15165 TT
1 TT
15167 TACTGATATT
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 58 1.00
ACGTcount: A:0.23, C:0.10, G:0.18, T:0.48
Consensus pattern (57 bp):
TTATGTTGGTATTAAACTGTTGGTTGATCAGTTTCATTTTGTATTTTCTACAAGCAA
Found at i:30416 original size:14 final size:16
Alignment explanation
Indices: 30395--30433 Score: 55
Period size: 14 Copynumber: 2.6 Consensus size: 16
30385 TTATTTCTTG
30395 AAATATTTTT-ATA-A
1 AAATATTTTTAATATA
*
30409 ATATATTTTTAATATA
1 AAATATTTTTAATATA
30425 AAATATTTT
1 AAATATTTT
30434 CATTCACTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 9 0.43
15 3 0.14
16 9 0.43
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
AAATATTTTTAATATA
Found at i:31951 original size:15 final size:16
Alignment explanation
Indices: 31931--31967 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
31921 TCTCGAATAT
31931 TTTTTATA-ATAATTA
1 TTTTTATATATAATTA
31946 TTTTTA-ATATAATTA
1 TTTTTATATATAATTA
*
31961 TTCTTAT
1 TTTTTAT
31968 GTTTTAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
14 1 0.05
15 18 0.95
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (16 bp):
TTTTTATATATAATTA
Found at i:32242 original size:67 final size:67
Alignment explanation
Indices: 32163--32291 Score: 240
Period size: 67 Copynumber: 1.9 Consensus size: 67
32153 AATTTTAAAA
* *
32163 TTCTCCAATATATTTACCCAAACAAATAAATTCATTTTTAAAAATTTAAAAACTTTGATAAACAA
1 TTCTCCAATATATTTACCCAAACAAATAAATTCATTTTTAAAAATTAAAAAACCTTGATAAACAA
32228 GG
66 GG
32230 TTCTCCAATATATTTACCCAAACAAATAAATTCATTTTTAAAAATTAAAAAACCTTGATAAA
1 TTCTCCAATATATTTACCCAAACAAATAAATTCATTTTTAAAAATTAAAAAACCTTGATAAA
32292 AAAAATTCCC
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
67 60 1.00
ACGTcount: A:0.47, C:0.16, G:0.03, T:0.34
Consensus pattern (67 bp):
TTCTCCAATATATTTACCCAAACAAATAAATTCATTTTTAAAAATTAAAAAACCTTGATAAACAA
GG
Found at i:33087 original size:29 final size:27
Alignment explanation
Indices: 33014--33088 Score: 68
Period size: 26 Copynumber: 2.9 Consensus size: 27
33004 AGTTTCAAAA
*
33014 AAAAAATAAGTAATAATGTTTT-ATTT
1 AAAAAATAAATAATAATGTTTTAATTT
* * *
33040 GAATAA-AAA-AA-AATCTTTTAGAGTTT
1 AAAAAATAAATAATAATGTTTTA-A-TTT
33066 AAAAAATAAATAATAATGTTTTA
1 AAAAAATAAATAATAATGTTTTA
33089 TCATAAAATA
Statistics
Matches: 36, Mismatches: 7, Indels: 9
0.69 0.13 0.17
Matches are distributed among these distances:
23 7 0.19
24 2 0.06
25 3 0.08
26 11 0.31
27 3 0.08
28 2 0.06
29 8 0.22
ACGTcount: A:0.53, C:0.01, G:0.08, T:0.37
Consensus pattern (27 bp):
AAAAAATAAATAATAATGTTTTAATTT
Found at i:33934 original size:3 final size:3
Alignment explanation
Indices: 33926--33955 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
33916 CCTGTTCTGA
33926 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
33956 GGGAAATCAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
ATG
Done.