Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005383.1 Kokia drynarioides strain JFW-HI SEQ_119373, 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: 50543
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Warning! 29 characters in sequence are not A, C, G, or T
Found at i:3030 original size:3 final size:3
Alignment explanation
Indices: 3015--3051 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
3005 TGGGGTTGAA
*
3015 GCT GCT CCT GCT GCT GCT GCT GCT GCT GCT GCT GCT G
1 GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT G
3052 ATGATGATGG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.00, C:0.35, G:0.32, T:0.32
Consensus pattern (3 bp):
GCT
Found at i:8424 original size:16 final size:15
Alignment explanation
Indices: 8395--8444 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
8385 ATTTTTTTTC
*
8395 AAATCGAGTCGAGTG
1 AAATCGAATCGAGTG
*
8410 AAAT-GAAATTCGAGTC
1 AAATCG-AA-TCGAGTG
8426 AAATCGAATCGAGTG
1 AAATCGAATCGAGTG
8441 AAAT
1 AAAT
8445 TGTTCGAGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
14 1 0.03
15 15 0.52
16 12 0.41
17 1 0.03
ACGTcount: A:0.42, C:0.12, G:0.24, T:0.22
Consensus pattern (15 bp):
AAATCGAATCGAGTG
Found at i:8697 original size:19 final size:19
Alignment explanation
Indices: 8668--8723 Score: 71
Period size: 19 Copynumber: 3.0 Consensus size: 19
8658 TTTTTAAAAA
8668 ATAAA-ATTTAGAATTTTT
1 ATAAATATTTAGAATTTTT
8686 ATAAATATTTAGAA-TTTT
1 ATAAATATTTAGAATTTTT
* *
8704 AAAAATTATTTTGAATTTTT
1 ATAAA-TATTTAGAATTTTT
8724 TGTAATTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
18 13 0.39
19 16 0.48
20 4 0.12
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (19 bp):
ATAAATATTTAGAATTTTT
Found at i:15704 original size:19 final size:18
Alignment explanation
Indices: 15682--15726 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
15672 TTATTATATT
* *
15682 AATTTAATAATCATTAAAA
1 AATTTAAAAATC-TAAAAA
15701 AATTCTAAAAATCTAAAAA
1 AATT-TAAAAATCTAAAAA
15720 AATTTAA
1 AATTTAA
15727 CAGAAAAATC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 3 0.13
19 13 0.57
20 7 0.30
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (18 bp):
AATTTAAAAATCTAAAAA
Found at i:16290 original size:22 final size:22
Alignment explanation
Indices: 16258--16301 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
16248 GTCGATCACC
*
16258 ATGGCAGATGCAGGTGGCGACG
1 ATGGCACATGCAGGTGGCGACG
16280 ATGGCACATGCAGGTGGCGACG
1 ATGGCACATGCAGGTGGCGACG
16302 GTGCTACTGC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.23, C:0.20, G:0.43, T:0.14
Consensus pattern (22 bp):
ATGGCACATGCAGGTGGCGACG
Found at i:36522 original size:12 final size:13
Alignment explanation
Indices: 36494--36535 Score: 52
Period size: 12 Copynumber: 3.3 Consensus size: 13
36484 GATGAATGGC
36494 TAATTAACATAA-
1 TAATTAACATAAT
*
36506 AAATT-ACATAAT
1 TAATTAACATAAT
36518 TAATTAACATAAT
1 TAATTAACATAAT
36531 ATAAT
1 -TAAT
36536 CTTAACATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
11 6 0.24
12 8 0.32
13 7 0.28
14 4 0.16
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.36
Consensus pattern (13 bp):
TAATTAACATAAT
Done.