Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005703.1 Kokia drynarioides strain JFW-HI SEQ_119916, 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: 11979
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.36
Found at i:1061 original size:6 final size:6
Alignment explanation
Indices: 1052--1116 Score: 55
Period size: 6 Copynumber: 11.0 Consensus size: 6
1042 TGGGTTTTAT
* * *
1052 TTTAAA TTTAAAA TTTGAAA -ATAAT TTTAAA CTTAAA -TTAAA TTTAAA
1 TTTAAA TTT-AAA TTT-AAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
1100 TTTAAA -ATAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA
1117 GGGAGTATGG
Statistics
Matches: 47, Mismatches: 8, Indels: 8
0.75 0.13 0.13
Matches are distributed among these distances:
5 11 0.23
6 27 0.57
7 9 0.19
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (6 bp):
TTTAAA
Found at i:1099 original size:17 final size:17
Alignment explanation
Indices: 1054--1116 Score: 81
Period size: 17 Copynumber: 3.6 Consensus size: 17
1044 GGTTTTATTT
1054 TAAATTTAAAATTTGAAAA
1 TAAATTT-AAATTT-AAAA
* * *
1073 TAATTTTAAACTTAAAT
1 TAAATTTAAATTTAAAA
1090 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
1107 TAAATTTAAA
1 TAAATTTAAA
1117 GGGAGTATGG
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
17 27 0.71
18 5 0.13
19 6 0.16
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:5914 original size:21 final size:21
Alignment explanation
Indices: 5887--5940 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
5877 GGAGTTTTTA
*
5887 GTATCGGTGGAAG-TATAACTT
1 GTATCGGTAGAAGTTAT-ACTT
*
5908 GTTTCGGTAGAAGTTATACTT
1 GTATCGGTAGAAGTTATACTT
5929 GTATCGGTAGAA
1 GTATCGGTAGAA
5941 CTATCACAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 26 0.90
22 3 0.10
ACGTcount: A:0.28, C:0.09, G:0.28, T:0.35
Consensus pattern (21 bp):
GTATCGGTAGAAGTTATACTT
Found at i:7068 original size:15 final size:15
Alignment explanation
Indices: 7048--7077 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
7038 CCTTAGTTTT
7048 ATTTTCTCTATCCTC
1 ATTTTCTCTATCCTC
*
7063 ATTTTCTCTCTCCTC
1 ATTTTCTCTATCCTC
7078 CAACATGAAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.10, C:0.37, G:0.00, T:0.53
Consensus pattern (15 bp):
ATTTTCTCTATCCTC
Found at i:9016 original size:27 final size:26
Alignment explanation
Indices: 8969--9031 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 26
8959 AATTTTAATA
* *
8969 AAAAAATATAATATATTTAAAAATTAT
1 AAAAAAT-TAAAATATTTAAAAATCAT
8996 AAAAAATTAAAAT-TTTATAAAGATCAT
1 AAAAAATTAAAATATTTA-AAA-ATCAT
9023 AAAAAATTA
1 AAAAAATTA
9032 TAAAATATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
25 4 0.12
26 8 0.25
27 20 0.62
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (26 bp):
AAAAAATTAAAATATTTAAAAATCAT
Found at i:9371 original size:28 final size:29
Alignment explanation
Indices: 9336--9438 Score: 100
Period size: 29 Copynumber: 3.5 Consensus size: 29
9326 AAAAAATTTC
*
9336 TAATTTTTAATAAAATTTAAATATTTTTTA
1 TAATTTTTAATAAAATTT-AATAATTTTTA
* *
9366 T-ATTTTTATTAAAATTTAGTAATTTTTA
1 TAATTTTTAATAAAATTTAATAATTTTTA
* *** *
9394 TAATTTTTATTATTTTTTAATATATTTTTC
1 TAATTTTTAATAAAATTTAATA-ATTTTTA
*
9424 TAGTTTTTAATAAAA
1 TAATTTTTAATAAAA
9439 GTAGGAGTTT
Statistics
Matches: 58, Mismatches: 13, Indels: 4
0.77 0.17 0.05
Matches are distributed among these distances:
28 10 0.17
29 31 0.53
30 17 0.29
ACGTcount: A:0.37, C:0.01, G:0.02, T:0.60
Consensus pattern (29 bp):
TAATTTTTAATAAAATTTAATAATTTTTA
Found at i:9393 original size:10 final size:9
Alignment explanation
Indices: 9360--9414 Score: 51
Period size: 9 Copynumber: 6.1 Consensus size: 9
9350 ATTTAAATAT
9360 TTTTTAT-A
1 TTTTTATAA
9368 TTTTTATTAA
1 TTTTTA-TAA
**
9378 AATTTAGTAA
1 TTTTTA-TAA
9388 TTTTTATAA
1 TTTTTATAA
*
9397 TTTTTATTA
1 TTTTTATAA
9406 TTTTT-TAA
1 TTTTTATAA
9414 T
1 T
9415 ATATTTTTCT
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
8 9 0.24
9 17 0.45
10 12 0.32
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (9 bp):
TTTTTATAA
Found at i:9867 original size:30 final size:28
Alignment explanation
Indices: 9833--9895 Score: 90
Period size: 30 Copynumber: 2.2 Consensus size: 28
9823 ATTTATTCTC
* *
9833 GTAAAAGAAAAAGTAAATACATTTTTTTGG
1 GTAAAAAAAAAAGTAAAT--ATATTTTTGG
9863 GTAAAAAAAAAAGTAAATATATTTTTGG
1 GTAAAAAAAAAAGTAAATATATTTTTGG
9891 GTAAA
1 GTAAA
9896 CTATAGAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
28 14 0.45
30 17 0.55
ACGTcount: A:0.51, C:0.02, G:0.16, T:0.32
Consensus pattern (28 bp):
GTAAAAAAAAAAGTAAATATATTTTTGG
Done.