Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006927.1 Kokia drynarioides strain JFW-HI SEQ_121530, 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: 25929
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.34
Warning! 82 characters in sequence are not A, C, G, or T
Found at i:12262 original size:104 final size:103
Alignment explanation
Indices: 12083--12280 Score: 222
Period size: 104 Copynumber: 1.9 Consensus size: 103
12073 TTATATTTAC
* * * * * *
12083 AAAAAATAATGATATTTGAACTAATTAATTGATTCTATAATTTAGAATTTATCATATTCATAATA
1 AAAAAATAATGATATTTGAAATAATTAATTAATTCTATAATTTAAAATTCATCATACTCACAATA
*
12148 TAGATGAAAAACAAT-GATATTTAAAATATTTACATATA
66 TAGATGAAAAA-AATAAATATTTAAAATATTTACATATA
* * *
12186 AAAATAATAATTATATTT-ATAATAATTATTTAATTTTATAATATTAAAATTCATCATACTCACA
1 AAAA-AATAATGATATTTGA-AATAATTAATTAATTCTATAAT-TTAAAATTCATCATACTCACA
* * *
12250 ATTTAGGT-AAAAAAATAAATATTTAACATAT
63 ATATAGATGAAAAAAATAAATATTTAAAATAT
12281 AGAAATTATA
Statistics
Matches: 78, Mismatches: 13, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
103 8 0.10
104 47 0.60
105 23 0.29
ACGTcount: A:0.49, C:0.06, G:0.05, T:0.40
Consensus pattern (103 bp):
AAAAAATAATGATATTTGAAATAATTAATTAATTCTATAATTTAAAATTCATCATACTCACAATA
TAGATGAAAAAAATAAATATTTAAAATATTTACATATA
Found at i:14266 original size:102 final size:102
Alignment explanation
Indices: 14090--14288 Score: 319
Period size: 102 Copynumber: 2.0 Consensus size: 102
14080 ATACTAAGAT
* * * **
14090 AAGTGCAACTTAACAAGTAAATGTCTTCAAAATAATAACAACATTAACGATAAAATAAGTGTTAT
1 AAGTGCAACTTAACAAGCAAATGTCTTCAAAATAATAACAAAATTAACGATAAAACAAAAGTTAT
14155 ACAATATCTAAATATTAACAACAAAATAGTAGCAATC
66 ACAATATCTAAATATTAACAACAAAATAGTAGCAATC
*
14192 AAGTGCAACTTAACAAGCAAATGTTTTCAAAATAATAACAAAATTAGA-GATAAAACAAAAGTTA
1 AAGTGCAACTTAACAAGCAAATGTCTTCAAAATAATAACAAAATTA-ACGATAAAACAAAAGTTA
*
14256 TACAATATCTAAATATTAATAACAAAATAGTAG
65 TACAATATCTAAATATTAACAACAAAATAGTAG
14289 TAACATAATG
Statistics
Matches: 89, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
102 88 0.99
103 1 0.01
ACGTcount: A:0.53, C:0.12, G:0.09, T:0.26
Consensus pattern (102 bp):
AAGTGCAACTTAACAAGCAAATGTCTTCAAAATAATAACAAAATTAACGATAAAACAAAAGTTAT
ACAATATCTAAATATTAACAACAAAATAGTAGCAATC
Found at i:17328 original size:20 final size:20
Alignment explanation
Indices: 17284--17328 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
17274 TTTTTCAACA
* *
17284 AAAAATTATAAAATTTTTTT
1 AAAAATTATAAAATATTTAT
* *
17304 CAAAATTTTAAAATATTTAT
1 AAAAATTATAAAATATTTAT
17324 AAAAA
1 AAAAA
17329 ATTCAAAATT
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (20 bp):
AAAAATTATAAAATATTTAT
Found at i:18351 original size:15 final size:15
Alignment explanation
Indices: 18331--18361 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
18321 TGAGTATTTT
18331 TTTAATTTCAAAATG
1 TTTAATTTCAAAATG
18346 TTTAATTTCAAAATG
1 TTTAATTTCAAAATG
18361 T
1 T
18362 CTCACACCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.39, C:0.06, G:0.06, T:0.48
Consensus pattern (15 bp):
TTTAATTTCAAAATG
Found at i:24001 original size:28 final size:31
Alignment explanation
Indices: 23954--24014 Score: 83
Period size: 28 Copynumber: 2.1 Consensus size: 31
23944 AGCTTATATA
23954 TTTATAATTTTTAAAAGGTT-AAAT-TAATT
1 TTTATAATTTTTAAAAGGTTAAAATGTAATT
**
23983 TTTAT-ATTTTTAATGGGTTAAAATGTAATT
1 TTTATAATTTTTAAAAGGTTAAAATGTAATT
24013 TT
1 TT
24015 ACTTTTACTA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 12 0.43
29 9 0.32
30 7 0.25
ACGTcount: A:0.36, C:0.00, G:0.10, T:0.54
Consensus pattern (31 bp):
TTTATAATTTTTAAAAGGTTAAAATGTAATT
Done.