Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006545.1 Kokia drynarioides strain JFW-HI SEQ_121130, 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: 31442
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.32
Found at i:3076 original size:18 final size:19
Alignment explanation
Indices: 3030--3080 Score: 63
Period size: 18 Copynumber: 2.8 Consensus size: 19
3020 TAAAAAAATT
3030 TAAT-AAATAAAATATATA
1 TAATAAAATAAAATATATA
*
3048 TAA-AATTATAAAATAT-TA
1 TAATAA-AATAAAATATATA
3066 TAATAAAATAAAATA
1 TAATAAAATAAAATA
3081 AAATAAATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
18 17 0.61
19 11 0.39
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (19 bp):
TAATAAAATAAAATATATA
Found at i:7281 original size:14 final size:14
Alignment explanation
Indices: 7262--7288 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
7252 TGAATGTAAC
7262 AAAATTTTCAAACA
1 AAAATTTTCAAACA
7276 AAAATTTTCAAAC
1 AAAATTTTCAAAC
7289 GCATTTGCAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.56, C:0.15, G:0.00, T:0.30
Consensus pattern (14 bp):
AAAATTTTCAAACA
Found at i:7906 original size:21 final size:21
Alignment explanation
Indices: 7882--7927 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
7872 TTCTCTTTCA
*
7882 CCTCTTCAACA-CGAACTTCCT
1 CCTCTCCAACATC-AACTTCCT
7903 CCTCTCCAACATCAACTTCCT
1 CCTCTCCAACATCAACTTCCT
7924 CCTC
1 CCTC
7928 AACAACAAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 22 0.96
22 1 0.04
ACGTcount: A:0.22, C:0.48, G:0.02, T:0.28
Consensus pattern (21 bp):
CCTCTCCAACATCAACTTCCT
Found at i:7933 original size:21 final size:21
Alignment explanation
Indices: 7895--7934 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
7885 CTTCAACACG
**
7895 AACTTCCTCCTCTCCAACATC
1 AACTTCCTCCTCAACAACATC
7916 AACTTCCTCCTCAACAACA
1 AACTTCCTCCTCAACAACA
7935 AGTTCTTCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.45, G:0.00, T:0.25
Consensus pattern (21 bp):
AACTTCCTCCTCAACAACATC
Found at i:11086 original size:27 final size:27
Alignment explanation
Indices: 11050--11105 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
11040 GGTTTTGCTC
11050 CCCTTATCCCACTTTCTTCAATTAACT
1 CCCTTATCCCACTTTCTTCAATTAACT
11077 CCCTTATCCCACTTTCTTCAATTAACT
1 CCCTTATCCCACTTTCTTCAATTAACT
11104 CC
1 CC
11106 AATGCATATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.21, C:0.39, G:0.00, T:0.39
Consensus pattern (27 bp):
CCCTTATCCCACTTTCTTCAATTAACT
Found at i:15228 original size:18 final size:19
Alignment explanation
Indices: 15194--15235 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
15184 TACATATATC
*
15194 AATTTTTATAATATTTA-A
1 AATTTTTAGAATATTTATA
15212 AATTTTTAGAACT-TTTATA
1 AATTTTTAGAA-TATTTATA
15231 AATTT
1 AATTT
15236 GCATCCATCT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 14 0.67
19 7 0.33
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.55
Consensus pattern (19 bp):
AATTTTTAGAATATTTATA
Found at i:17014 original size:25 final size:23
Alignment explanation
Indices: 16963--17017 Score: 60
Period size: 22 Copynumber: 2.4 Consensus size: 23
16953 ATAGTGTGTG
16963 ATATA-ATATTATATAATGAAAT
1 ATATATATATTATATAATGAAAT
* *
16985 A-ATATATATTATAAGTATTGATAT
1 ATATATATATTAT-A-TAATGAAAT
17009 ATATATATA
1 ATATATATA
17018 ACTATTATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
21 3 0.11
22 8 0.30
23 1 0.04
24 8 0.30
25 7 0.26
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (23 bp):
ATATATATATTATATAATGAAAT
Found at i:20065 original size:15 final size:15
Alignment explanation
Indices: 20045--20077 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
20035 GAACTATGAA
20045 ACTTAAGGTGCAAAT
1 ACTTAAGGTGCAAAT
20060 ACTTAAGGTGCAAAT
1 ACTTAAGGTGCAAAT
20075 ACT
1 ACT
20078 ATTAAGTCAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.39, C:0.15, G:0.18, T:0.27
Consensus pattern (15 bp):
ACTTAAGGTGCAAAT
Found at i:29896 original size:14 final size:14
Alignment explanation
Indices: 29877--29906 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
29867 GGTTCGGGTT
29877 AGGTTTAGGTCAAA
1 AGGTTTAGGTCAAA
*
29891 AGGTTTGGGTCAAA
1 AGGTTTAGGTCAAA
29905 AG
1 AG
29907 TTCGGTTTGG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.33, C:0.07, G:0.33, T:0.27
Consensus pattern (14 bp):
AGGTTTAGGTCAAA
Done.