Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011011.1 Kokia drynarioides strain JFW-HI SEQ_125981, 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: 33578
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:1341 original size:11 final size:11
Alignment explanation
Indices: 1322--1355 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
1312 ATAGTTCTCC
*
1322 AAAATCCTAAA
1 AAAAACCTAAA
1333 AAAAACCTAAA
1 AAAAACCTAAA
*
1344 AATAACCTAAA
1 AAAAACCTAAA
1355 A
1 A
1356 TTAATAAAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.68, C:0.18, G:0.00, T:0.15
Consensus pattern (11 bp):
AAAAACCTAAA
Found at i:1510 original size:23 final size:23
Alignment explanation
Indices: 1457--1514 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 23
1447 TTGTCCATCT
*
1457 TTGCTGACTAGACCTTCTGGAAG
1 TTGCTGACTAGACCTTCTAGAAG
* ** * *
1480 CTATTGACTGGATCTTCTAGAAG
1 TTGCTGACTAGACCTTCTAGAAG
1503 TTGCTGACTAGA
1 TTGCTGACTAGA
1515 TTCCATGTCA
Statistics
Matches: 25, Mismatches: 10, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.33
Consensus pattern (23 bp):
TTGCTGACTAGACCTTCTAGAAG
Found at i:2278 original size:20 final size:19
Alignment explanation
Indices: 2250--2288 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
2240 GTTTAAGCAA
*
2250 CCATGTTTTTTCTTCTTTTT
1 CCATGTTTTCTC-TCTTTTT
*
2270 CCATTTTTTCTCTCTTTTT
1 CCATGTTTTCTCTCTTTTT
2289 TTCTTTTCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.05, C:0.23, G:0.03, T:0.69
Consensus pattern (19 bp):
CCATGTTTTCTCTCTTTTT
Found at i:3343 original size:5 final size:5
Alignment explanation
Indices: 3328--3367 Score: 55
Period size: 5 Copynumber: 7.8 Consensus size: 5
3318 ATTAATGATG
3328 AAAACT AAAAT AAAAT AAAAT AAAAT AATAA- AAAAT AAAA
1 AAAA-T AAAAT AAAAT AAAAT AAAAT AA-AAT AAAAT AAAA
3368 AACAATGGGT
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
4 2 0.06
5 24 0.75
6 6 0.19
ACGTcount: A:0.80, C:0.03, G:0.00, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:4617 original size:23 final size:23
Alignment explanation
Indices: 4591--4636 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
4581 CTGATTAGAC
4591 CTTCTGAAAGCTACTGACTGGAT
1 CTTCTGAAAGCTACTGACTGGAT
* **
4614 CTTCTGGAAGCTGTTGACTGGAT
1 CTTCTGAAAGCTACTGACTGGAT
4637 GCCACGTCAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.22, C:0.20, G:0.26, T:0.33
Consensus pattern (23 bp):
CTTCTGAAAGCTACTGACTGGAT
Found at i:13731 original size:3 final size:3
Alignment explanation
Indices: 13723--13747 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
13713 TTGCGGCACT
13723 TGC TGC TGC TGC TGC TGC TGC TGC T
1 TGC TGC TGC TGC TGC TGC TGC TGC T
13748 CGACCTCCCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.32, T:0.36
Consensus pattern (3 bp):
TGC
Found at i:25893 original size:14 final size:14
Alignment explanation
Indices: 25869--25911 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
25859 AACATTATAT
25869 ATATAATTTTTACAA
1 ATAT-ATTTTTACAA
*
25884 ATATATTTTTACAT
1 ATATATTTTTACAA
25898 ATAT-TTTTTACAA
1 ATATATTTTTACAA
25911 A
1 A
25912 GCTGTGTCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
13 9 0.35
14 13 0.50
15 4 0.15
ACGTcount: A:0.42, C:0.07, G:0.00, T:0.51
Consensus pattern (14 bp):
ATATATTTTTACAA
Done.