Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011589.1 Kokia drynarioides strain JFW-HI SEQ_126579, 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: 10005
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.35
Warning! 84 characters in sequence are not A, C, G, or T
Found at i:2781 original size:71 final size:71
Alignment explanation
Indices: 2699--2841 Score: 259
Period size: 71 Copynumber: 2.0 Consensus size: 71
2689 TCTATATAAG
* * *
2699 ATTTGCTTTGATATATGATATACCAAACTTGTTAGCTTATGATAGCCATTCTCCATAATCATGTC
1 ATTTGCTTTGATATATAACATACCAAACTTGTTAGCTTATGATAGCCACTCTCCATAATCATGTC
2764 CCTTAC
66 CCTTAC
2770 ATTTGCTTTGATATATAACATACCAAACTTGTTAGCTTATGATAGCCACTCTCCATAATCATGTC
1 ATTTGCTTTGATATATAACATACCAAACTTGTTAGCTTATGATAGCCACTCTCCATAATCATGTC
2835 CCTTAC
66 CCTTAC
2841 A
1 A
2842 AATTTACTTA
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
71 69 1.00
ACGTcount: A:0.29, C:0.22, G:0.10, T:0.38
Consensus pattern (71 bp):
ATTTGCTTTGATATATAACATACCAAACTTGTTAGCTTATGATAGCCACTCTCCATAATCATGTC
CCTTAC
Found at i:5571 original size:33 final size:33
Alignment explanation
Indices: 5529--5593 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
5519 AAACTTTTTA
*
5529 TTTTTATTTT-TCAT-TTTTATATTCAAAAAATAT
1 TTTTTATTTTCT-ATCTTTTAAATT-AAAAAATAT
5562 TTTTTATTTTCTATCTTTTAAATTAAAAAATA
1 TTTTTATTTTCTATCTTTTAAATTAAAAAATA
5594 CATTTGATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
33 20 0.69
34 9 0.31
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.58
Consensus pattern (33 bp):
TTTTTATTTTCTATCTTTTAAATTAAAAAATAT
Found at i:9468 original size:93 final size:95
Alignment explanation
Indices: 9361--9554 Score: 295
Period size: 96 Copynumber: 2.1 Consensus size: 95
9351 TGAATAAAAG
* *
9361 TTTTTTTTACATCATTTATAT-A-A-TATTAGAAAGGTATAATGACAAAAATAGTCCCTAACGTT
1 TTTTTTTTACATCATTTATATAATATTATTAGAAAGGTATAATGACAAAAACAGTCCCTAACATT
* *
9423 TAGGTGTTGGGTTACTTTGACTCTTAATGT
66 TAAGTGTTGGGTCACTTTGACTCTTAATGT
*
9453 TTTTTTTTAACATCATTTATATAATATTATTAGAAAGGTATAATGACAAAAACAGTCTCTAACAT
1 TTTTTTTT-ACATCATTTATATAATATTATTAGAAAGGTATAATGACAAAAACAGTCCCTAACAT
* *
9518 TTAAGTGTTGGGTCACTTTGATTTTTAATGT
65 TTAAGTGTTGGGTCACTTTGACTCTTAATGT
9549 TTTTTT
1 TTTTTT
9555 GGAGCACTTT
Statistics
Matches: 91, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
92 8 0.09
93 13 0.14
94 1 0.01
95 1 0.01
96 68 0.75
ACGTcount: A:0.32, C:0.10, G:0.13, T:0.45
Consensus pattern (95 bp):
TTTTTTTTACATCATTTATATAATATTATTAGAAAGGTATAATGACAAAAACAGTCCCTAACATT
TAAGTGTTGGGTCACTTTGACTCTTAATGT
Done.