Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006421.1 Kokia drynarioides strain JFW-HI SEQ_121002, 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: 19064
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Found at i:3266 original size:67 final size:69
Alignment explanation
Indices: 3181--3312 Score: 180
Period size: 69 Copynumber: 1.9 Consensus size: 69
3171 ATAAACAATA
* * *
3181 TAATGGTTTTGCATTTTAAC-TT-AATGGGTAAACATTTATCAAAATGACATAATTTTATCTTTT
1 TAATGGTTTTGCATTTTAACTTTGAAAGGGTAAACATTTATCAAAAAGACATAATTTTACCTTTT
3244 AACT
66 AACT
* * *
3248 TAATGGTTTTG-ACTTTTAACTTTGAAAGGGTAAATATTTATCAAAAAGACGTAGTTTTACCTTT
1 TAATGGTTTTGCA-TTTTAACTTTGAAAGGGTAAACATTTATCAAAAAGACATAATTTTACCTTT
3312 T
65 T
3313 TTTATTAGGA
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
66 1 0.02
67 18 0.32
68 2 0.04
69 35 0.62
ACGTcount: A:0.33, C:0.10, G:0.13, T:0.44
Consensus pattern (69 bp):
TAATGGTTTTGCATTTTAACTTTGAAAGGGTAAACATTTATCAAAAAGACATAATTTTACCTTTT
AACT
Found at i:8298 original size:2 final size:2
Alignment explanation
Indices: 8291--8324 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
8281 GAATCCCGTC
8291 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
8325 CATTTCTCTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:10506 original size:54 final size:54
Alignment explanation
Indices: 10443--10551 Score: 209
Period size: 54 Copynumber: 2.0 Consensus size: 54
10433 AAATATCTTC
*
10443 CATTAAGAGTGTTAGGACCATTAATTTTCCTGTTTTTCTACATGTCCTTGTTTA
1 CATTAAGAGTGTTAGGACCATTAATTTTCATGTTTTTCTACATGTCCTTGTTTA
10497 CATTAAGAGTGTTAGGACCATTAATTTTCATGTTTTTCTACATGTCCTTGTTTA
1 CATTAAGAGTGTTAGGACCATTAATTTTCATGTTTTTCTACATGTCCTTGTTTA
10551 C
1 C
10552 GTAGTGAATT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.23, C:0.17, G:0.15, T:0.46
Consensus pattern (54 bp):
CATTAAGAGTGTTAGGACCATTAATTTTCATGTTTTTCTACATGTCCTTGTTTA
Found at i:18964 original size:21 final size:22
Alignment explanation
Indices: 18930--19064 Score: 130
Period size: 23 Copynumber: 5.9 Consensus size: 22
18920 GGAACAAACT
* *
18930 GAGAGTAC-CAAAGTACTAACA
1 GAGAGCACACAAAGTGCTAACA
* *
18951 GAGAGCACA-TAAGTGCTGGGCAATA
1 GAGAGCACACAAAGTGCT----AACA
* *
18976 GAGAGAACACACAGTGCTAAACA
1 GAGAGCACACAAAGTGCT-AACA
18999 GAGAGCACACAAAGTGCTAATCA
1 GAGAGCACACAAAGTGCTAA-CA
19022 GAGAGCACACAAAGTGCTAATCA
1 GAGAGCACACAAAGTGCTAA-CA
*
19045 GAGAGCACACACAGTGCTAA
1 GAGAGCACACAAAGTGCTAA
Statistics
Matches: 95, Mismatches: 12, Indels: 12
0.80 0.10 0.10
Matches are distributed among these distances:
21 13 0.14
22 2 0.02
23 63 0.66
25 11 0.12
26 6 0.06
ACGTcount: A:0.43, C:0.21, G:0.24, T:0.13
Consensus pattern (22 bp):
GAGAGCACACAAAGTGCTAACA
Found at i:19003 original size:23 final size:23
Alignment explanation
Indices: 18975--19064 Score: 144
Period size: 23 Copynumber: 3.9 Consensus size: 23
18965 GCTGGGCAAT
* * *
18975 AGAGAGAACACACAGTGCTAAAC
1 AGAGAGCACACAAAGTGCTAATC
18998 AGAGAGCACACAAAGTGCTAATC
1 AGAGAGCACACAAAGTGCTAATC
19021 AGAGAGCACACAAAGTGCTAATC
1 AGAGAGCACACAAAGTGCTAATC
*
19044 AGAGAGCACACACAGTGCTAA
1 AGAGAGCACACAAAGTGCTAA
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 63 1.00
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.11
Consensus pattern (23 bp):
AGAGAGCACACAAAGTGCTAATC
Found at i:19049 original size:69 final size:66
Alignment explanation
Indices: 18925--19064 Score: 165
Period size: 69 Copynumber: 2.0 Consensus size: 66
18915 TATACGGAAC
* * *
18925 AAACTGAGAGTACCAAAGTACTAACAGAGAGCACATAAGTGCTGGGCAATAGAGAGAACACACAG
1 AAACAGAGAGCACCAAAGTACTAACAGAGAGCACAAAAGTGCT--G-AATAGAGAGAACACACAG
18990 TGCT
63 TGCT
* *
18994 AAACAGAGAGCACACAAAGTGCTAATCAGAGAGCACACAAAGTGCT-AATCAGAGAGCACACACA
1 AAACAGAGAGCAC-CAAAGTACTAA-CAGAGAGCACA-AAAGTGCTGAAT-AGAGAGAACACACA
19058 GTGCT
62 GTGCT
19063 AA
1 AA
Statistics
Matches: 62, Mismatches: 5, Indels: 8
0.83 0.07 0.11
Matches are distributed among these distances:
68 3 0.05
69 31 0.50
70 10 0.16
71 11 0.18
72 7 0.11
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.13
Consensus pattern (66 bp):
AAACAGAGAGCACCAAAGTACTAACAGAGAGCACAAAAGTGCTGAATAGAGAGAACACACAGTGC
T
Done.