Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014738.1 Kokia drynarioides strain JFW-HI SEQ_129777, 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: 1872
ACGTcount: A:0.35, C:0.11, G:0.13, T:0.38
Warning! 50 characters in sequence are not A, C, G, or T
Found at i:631 original size:18 final size:18
Alignment explanation
Indices: 610--732 Score: 67
Period size: 18 Copynumber: 6.8 Consensus size: 18
600 TTTTTGAGCA
610 TTTTATAATTTTTTATATT
1 TTTTATAATTTTTTATA-T
*
629 TTTTATGA-TTTTTATATT
1 TTTTATAATTTTTTATA-T
* * * *
647 TTTTCTAATCTTTGATAAA
1 TTTTATAATTTTTTAT-AT
666 TTTTA-AATTTTTTAT-T
1 TTTTATAATTTTTTATAT
** *
682 TTTTATTAAAATTTAATAAT
1 TTTTA-TAATTTTTTAT-AT
* *
702 TTTTAT--TTATTTATGT
1 TTTTATAATTTTTTATAT
718 TTTTATATATTTTTT
1 TTTTATA-ATTTTTT
733 GCCACATGTC
Statistics
Matches: 76, Mismatches: 19, Indels: 18
0.67 0.17 0.16
Matches are distributed among these distances:
16 12 0.16
17 4 0.05
18 31 0.41
19 22 0.29
20 7 0.09
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.68
Consensus pattern (18 bp):
TTTTATAATTTTTTATAT
Found at i:639 original size:27 final size:27
Alignment explanation
Indices: 609--732 Score: 85
Period size: 27 Copynumber: 4.6 Consensus size: 27
599 TTTTTTGAGC
*
609 ATTTTATAATTTTTTATATTTTTTATG
1 ATTTTATAATTTTTTATATTTTTTATA
* * *
636 ATTTT-TATATTTTTTCTAATCTTTGATAA
1 ATTTTATA-ATTTTTTAT-ATTTTTTAT-A
* *
665 ATTTTA-AATTTTTTATTTTTTATTAAA
1 ATTTTATAATTTTTTATATTTT-TTATA
* * *
692 ATTTAATAA-TTTTTAT-TTATTTATG
1 ATTTTATAATTTTTTATATTTTTTATA
*
717 TTTTTATATATTTTTT
1 ATTTTATA-ATTTTTT
733 GCCACATGTC
Statistics
Matches: 74, Mismatches: 15, Indels: 16
0.70 0.14 0.15
Matches are distributed among these distances:
25 9 0.12
26 6 0.08
27 34 0.46
28 19 0.26
29 6 0.08
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.68
Consensus pattern (27 bp):
ATTTTATAATTTTTTATATTTTTTATA
Found at i:641 original size:28 final size:28
Alignment explanation
Indices: 609--705 Score: 92
Period size: 28 Copynumber: 3.5 Consensus size: 28
599 TTTTTTGAGC
*
609 ATTTTATAATTTTTTATATTTTTTATGA
1 ATTTTATAATTTTTTATATTTTTTATAA
* * * *
637 TTTTTAT-ATTTTTTCTAATCTTTGATAA
1 ATTTTATAATTTTTTAT-ATTTTTTATAA
*
665 ATTTTA-AATTTTTTATTTTTTATTA-AA
1 ATTTTATAATTTTTTATATTTT-TTATAA
*
692 ATTTAATAATTTTT
1 ATTTTATAATTTTT
706 ATTTATTTAT
Statistics
Matches: 54, Mismatches: 11, Indels: 8
0.74 0.15 0.11
Matches are distributed among these distances:
27 18 0.33
28 36 0.67
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (28 bp):
ATTTTATAATTTTTTATATTTTTTATAA
Found at i:706 original size:10 final size:9
Alignment explanation
Indices: 610--707 Score: 65
Period size: 9 Copynumber: 10.7 Consensus size: 9
600 TTTTTGAGCA
610 TTTTATAATT
1 TTTTATAA-T
*
620 TTTTATATT
1 TTTTATAAT
*
629 TTTTATGAT
1 TTTTATAAT
*
638 TTTTATATT
1 TTTTATAAT
*
647 TTTTCTAAT
1 TTTTATAAT
* *
656 CTTTGATAAA
1 -TTTTATAAT
666 TTTTA-AAT
1 TTTTATAAT
*
674 TTTT-TATT
1 TTTTATAAT
*
682 TTTTATTAAAA
1 TTTTA-T-AAT
*
693 TTTAATAAT
1 TTTTATAAT
702 TTTTAT
1 TTTTAT
708 TTATTTATGT
Statistics
Matches: 65, Mismatches: 18, Indels: 11
0.69 0.19 0.12
Matches are distributed among these distances:
8 12 0.18
9 33 0.51
10 15 0.23
11 5 0.08
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (9 bp):
TTTTATAAT
Found at i:1175 original size:10 final size:11
Alignment explanation
Indices: 1146--1173 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
1136 ACTTAGAGGG
1146 TATTTTTGATA
1 TATTTTTGATA
1157 TATTTTTGATA
1 TATTTTTGATA
1168 TATTTT
1 TATTTT
1174 GAAAGTTCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.25, C:0.00, G:0.07, T:0.68
Consensus pattern (11 bp):
TATTTTTGATA
Done.