Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003640.1 Kokia drynarioides strain JFW-HI SEQ_116538, 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, 712
Length: 1188
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.31
Warning! 114 characters in sequence are not A, C, G, or T
Found at i:31 original size:7 final size:7
Alignment explanation
Indices: 6--129 Score: 64
Period size: 7 Copynumber: 17.7 Consensus size: 7
1 AACGT
6 ATTAATA
1 ATTAATA
* *
13 AGT-ATC
1 ATTAATA
19 ATTAATA
1 ATTAATA
26 ATTAATA
1 ATTAATA
33 A-TAATA
1 ATTAATA
39 A-TAATA
1 ATTAATA
* *
45 AATAACAA
1 ATTAA-TA
*
53 ATTTATA
1 ATTAATA
60 A-TAATGA
1 ATTAAT-A
67 TATTAATA
1 -ATTAATA
* *
75 AGTATTA
1 ATTAATA
82 A-TAGCAGTA
1 ATTA--A-TA
91 ATTAATA
1 ATTAATA
*
98 A-TACCT-
1 ATTA-ATA
104 ATTAATA
1 ATTAATA
111 ATTAATA
1 ATTAATA
118 ATTAATA
1 ATTAATA
125 ATTAA
1 ATTAA
130 ACCACGAACA
Statistics
Matches: 90, Mismatches: 14, Indels: 26
0.69 0.11 0.20
Matches are distributed among these distances:
6 25 0.28
7 49 0.54
8 7 0.08
9 7 0.08
10 2 0.02
ACGTcount: A:0.54, C:0.04, G:0.04, T:0.38
Consensus pattern (7 bp):
ATTAATA
Found at i:126 original size:10 final size:10
Alignment explanation
Indices: 21--119 Score: 51
Period size: 10 Copynumber: 9.4 Consensus size: 10
11 TAAGTATCAT
21 TAATAATTAA
1 TAATAATTAA
31 TAATAA-TAA
1 TAATAATTAA
*
40 TAATAAATAA
1 TAATAATTAA
* *
50 CAA-ATTTATAA
1 TAATA-AT-TAA
61 TAATGATATTAA
1 TAAT-A-ATTAA
73 TAAGT-ATTAA
1 TAA-TAATTAA
83 TAGCAGTAATTAA
1 TA--A-TAATTAA
** *
96 TAATACCTAT
1 TAATAATTAA
106 TAATAATTAA
1 TAATAATTAA
116 TAAT
1 TAAT
120 TAATAATTAA
Statistics
Matches: 69, Mismatches: 11, Indels: 18
0.70 0.11 0.18
Matches are distributed among these distances:
9 10 0.14
10 33 0.48
11 6 0.09
12 9 0.13
13 11 0.16
ACGTcount: A:0.55, C:0.04, G:0.04, T:0.37
Consensus pattern (10 bp):
TAATAATTAA
Found at i:1144 original size:30 final size:30
Alignment explanation
Indices: 1109--1176 Score: 102
Period size: 30 Copynumber: 2.3 Consensus size: 30
1099 CTAAACTTTA
1109 CAAAAATTCCATTTTTGACCC-CAAAACTTC
1 CAAAAATTCCATTTTT-ACCCTCAAAACTTC
**
1139 CAAAAATTCCATTTTTACCCTTGAAACTTC
1 CAAAAATTCCATTTTTACCCTCAAAACTTC
1169 CAAAAATT
1 CAAAAATT
1177 ATATTTTACC
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
29 4 0.11
30 31 0.89
ACGTcount: A:0.38, C:0.26, G:0.03, T:0.32
Consensus pattern (30 bp):
CAAAAATTCCATTTTTACCCTCAAAACTTC
Found at i:1158 original size:29 final size:29
Alignment explanation
Indices: 1109--1188 Score: 101
Period size: 30 Copynumber: 2.7 Consensus size: 29
1099 CTAAACTTTA
1109 CAAAAATTCCATTTTTGACCCCAAAACTTC
1 CAAAAATTCCATTTTT-ACCCCAAAACTTC
**
1139 CAAAAATTCCATTTTTACCCTTGAAACTTC
1 CAAAAATTCCATTTTTACCC-CAAAACTTC
1169 CAAAAATT--ATATTTTACCCC
1 CAAAAATTCCAT-TTTTACCCC
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
28 2 0.04
29 12 0.27
30 31 0.69
ACGTcount: A:0.36, C:0.28, G:0.03, T:0.34
Consensus pattern (29 bp):
CAAAAATTCCATTTTTACCCCAAAACTTC
Done.