Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008629.1 Kokia drynarioides strain JFW-HI SEQ_123308, 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: 3885
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.34
Found at i:14 original size:9 final size:9
Alignment explanation
Indices: 1--44 Score: 56
Period size: 9 Copynumber: 5.0 Consensus size: 9
1 TTATAAAAA
1 TTATAAAAA
10 TTATAATAAA
1 TTATAA-AAA
*
20 TTTTAAAAA
1 TTATAAAAA
29 --ATAAAAA
1 TTATAAAAA
36 TTATAAAAA
1 TTATAAAAA
45 ATCATTTAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
7 6 0.20
9 16 0.53
10 8 0.27
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (9 bp):
TTATAAAAA
Found at i:283 original size:18 final size:16
Alignment explanation
Indices: 268--298 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
258 AAATTTTATT
268 ATACTTTAATATTTTA
1 ATACTTTAATATTTTA
*
284 ATATTTTAATATTTT
1 ATACTTTAATATTTT
299 TAAAAGATTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.61
Consensus pattern (16 bp):
ATACTTTAATATTTTA
Found at i:301 original size:9 final size:8
Alignment explanation
Indices: 272--298 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
262 TTTATTATAC
272 TTTAATAT
1 TTTAATAT
280 TTTAATAT
1 TTTAATAT
288 TTTAATAT
1 TTTAATAT
296 TTT
1 TTT
299 TAAAAGATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (8 bp):
TTTAATAT
Found at i:320 original size:30 final size:30
Alignment explanation
Indices: 281--380 Score: 98
Period size: 30 Copynumber: 3.3 Consensus size: 30
271 CTTTAATATT
*
281 TTAATATTTTA-ATATTTTTAAAAGATTAAA
1 TTAAAATTTTATA-ATTTTTAAAAGATTAAA
* *
311 TTAAAATTTTATCATTTTTAAAA-AATAAA
1 TTAAAATTTTATAATTTTTAAAAGATTAAA
* * *
340 ATAAAATATTATAATTTTT-AAAGCATCAAA
1 TTAAAATTTTATAATTTTTAAAAG-ATTAAA
370 TATAAAATTTT
1 T-TAAAATTTT
381 CTAAAAGGCC
Statistics
Matches: 56, Mismatches: 10, Indels: 7
0.77 0.14 0.10
Matches are distributed among these distances:
28 3 0.05
29 21 0.38
30 24 0.43
31 8 0.14
ACGTcount: A:0.50, C:0.03, G:0.02, T:0.45
Consensus pattern (30 bp):
TTAAAATTTTATAATTTTTAAAAGATTAAA
Found at i:344 original size:29 final size:28
Alignment explanation
Indices: 286--380 Score: 91
Period size: 29 Copynumber: 3.2 Consensus size: 28
276 ATATTTTAAT
* *
286 ATTTTAATATTTTTAAAAGATTAAATTAAA
1 ATTTT-ATATTTTTAAAA-AATAAAATAAA
316 ATTTTATCATTTTTAAAAAATAAAATAAA
1 ATTTTAT-ATTTTTAAAAAATAAAATAAA
* **
345 ATATTATAATTTTTAAAGCATCAAATATAAA
1 ATTTTAT-ATTTTTAAAAAAT-AAA-ATAAA
376 ATTTT
1 ATTTT
381 CTAAAAGGCC
Statistics
Matches: 55, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
29 28 0.51
30 18 0.33
31 9 0.16
ACGTcount: A:0.51, C:0.03, G:0.02, T:0.44
Consensus pattern (28 bp):
ATTTTATATTTTTAAAAAATAAAATAAA
Found at i:890 original size:35 final size:34
Alignment explanation
Indices: 850--915 Score: 91
Period size: 33 Copynumber: 1.9 Consensus size: 34
840 TCATAATTGT
850 TTTTAATTTAATTTATACTTATAT-AAT-TTTTTGAA
1 TTTTAA-TT-ATTTATA-TTATATGAATATTTTTGAA
885 TTTTAATTATTTATATTATATGAATATTTTT
1 TTTTAATTATTTATATTATATGAATATTTTT
916 TTGAATATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
32 6 0.21
33 10 0.34
34 7 0.24
35 6 0.21
ACGTcount: A:0.33, C:0.02, G:0.03, T:0.62
Consensus pattern (34 bp):
TTTTAATTATTTATATTATATGAATATTTTTGAA
Found at i:916 original size:35 final size:36
Alignment explanation
Indices: 850--921 Score: 89
Period size: 36 Copynumber: 2.0 Consensus size: 36
840 TCATAATTGT
850 TTTTAATTTAATTTATACTTATATAA-TTTTTTGAA
1 TTTTAATTTAATTTATACTTATATAATTTTTTTGAA
885 TTTTAA-TT-ATTTATA-TTATATGAATATTTTTTTGAA
1 TTTTAATTTAATTTATACTTATAT--A-ATTTTTTTGAA
921 T
1 T
922 ATATTTGTGT
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
32 6 0.18
33 7 0.21
34 3 0.09
35 7 0.21
36 10 0.30
ACGTcount: A:0.33, C:0.01, G:0.04, T:0.61
Consensus pattern (36 bp):
TTTTAATTTAATTTATACTTATATAATTTTTTTGAA
Done.