Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008380.1 Kokia drynarioides strain JFW-HI SEQ_123048, 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: 3122
ACGTcount: A:0.35, C:0.14, G:0.13, T:0.38
Found at i:1375 original size:28 final size:28
Alignment explanation
Indices: 1326--1389 Score: 78
Period size: 28 Copynumber: 2.3 Consensus size: 28
1316 CTAAAACTTT
1326 AAAATTTAGCTCTTATATTTTTAATTTAA
1 AAAATTTAGCTCTTATATTTTTAATTT-A
* *
1355 AAAATTTAG-TCTTA-ATTTTTTTATTTC
1 AAAATTTAGCTCTTATA-TTTTTAATTTA
1382 AAAATTTA
1 AAAATTTA
1390 AATTCAACTG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
27 9 0.28
28 14 0.44
29 9 0.28
ACGTcount: A:0.38, C:0.06, G:0.03, T:0.53
Consensus pattern (28 bp):
AAAATTTAGCTCTTATATTTTTAATTTA
Found at i:1375 original size:29 final size:27
Alignment explanation
Indices: 1326--1389 Score: 76
Period size: 29 Copynumber: 2.3 Consensus size: 27
1316 CTAAAACTTT
1326 AAAATTTAGCTCTTATATTTTTAATTTAA
1 AAAATTTAGCTCTTATATTTTT-ATTT-A
* *
1355 AAAATTTAG-TCTTAATTTTTTTATTTC
1 AAAATTTAGCTCTT-ATATTTTTATTTA
1382 AAAATTTA
1 AAAATTTA
1390 AATTCAACTG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
27 8 0.25
28 8 0.25
29 16 0.50
ACGTcount: A:0.38, C:0.06, G:0.03, T:0.53
Consensus pattern (27 bp):
AAAATTTAGCTCTTATATTTTTATTTA
Found at i:1869 original size:26 final size:25
Alignment explanation
Indices: 1832--1884 Score: 79
Period size: 26 Copynumber: 2.1 Consensus size: 25
1822 GAAATTGATA
1832 TTTTTTTCTAATTTGATATTTAAAT
1 TTTTTTTCTAATTTGATATTTAAAT
* *
1857 TTTTTTATTTAATTTGGTATTTAAAT
1 TTTTTT-TCTAATTTGATATTTAAAT
1883 TT
1 TT
1885 AATAATTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 6 0.24
26 19 0.76
ACGTcount: A:0.26, C:0.02, G:0.06, T:0.66
Consensus pattern (25 bp):
TTTTTTTCTAATTTGATATTTAAAT
Found at i:1892 original size:26 final size:26
Alignment explanation
Indices: 1840--1892 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
1830 TATTTTTTTC
** *
1840 TAATTTGATATTTAAATTTTTTTATT
1 TAATTTGATATTTAAATTTAATAATT
*
1866 TAATTTGGTATTTAAATTTAATAATT
1 TAATTTGATATTTAAATTTAATAATT
1892 T
1 T
1893 TTCTTTGGTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.60
Consensus pattern (26 bp):
TAATTTGATATTTAAATTTAATAATT
Found at i:2997 original size:8 final size:9
Alignment explanation
Indices: 2820--3001 Score: 61
Period size: 9 Copynumber: 19.6 Consensus size: 9
2810 TTTTCTCATA
*
2820 AAAAATCAT
1 AAAAATTAT
*
2829 ATAAATTAT
1 AAAAATTAT
*
2838 AAAAA-AAT
1 AAAAATTAT
2846 AAAAA-TATT
1 AAAAATTA-T
* *
2855 AAAACTAAT
1 AAAAATTAT
2864 ATAAAATTAT
1 A-AAAATTAT
**
2874 ACCAATTAT
1 AAAAATTAT
*
2883 AAAACTTAT
1 AAAAATTAT
*
2892 ATAAAATCAT
1 A-AAAATTAT
2902 AAAAAACTTAT
1 -AAAAA-TTAT
*
2913 AAAAAAATTCT
1 --AAAAATTAT
** *
2924 -ACTAGTA-
1 AAAAATTAT
*
2931 ATAAATTAT
1 AAAAATTAT
2940 AAAACATT-T
1 AAAA-ATTAT
*
2949 AAAATTTTAT
1 AAAA-ATTAT
*
2959 AAAAACTTGT
1 AAAAA-TTAT
*
2969 AAGAATTCAT
1 AAAAATT-AT
2979 AAAAAATTAT
1 -AAAAATTAT
2989 AAAAA-TAT
1 AAAAATTAT
2997 AAAAA
1 AAAAA
3002 ATTCTAATAA
Statistics
Matches: 125, Mismatches: 34, Indels: 29
0.66 0.18 0.15
Matches are distributed among these distances:
8 22 0.18
9 48 0.38
10 36 0.29
11 13 0.10
12 6 0.05
ACGTcount: A:0.61, C:0.07, G:0.02, T:0.31
Consensus pattern (9 bp):
AAAAATTAT
Found at i:3000 original size:18 final size:20
Alignment explanation
Indices: 2977--3020 Score: 65
Period size: 18 Copynumber: 2.3 Consensus size: 20
2967 GTAAGAATTC
2977 ATAAAAAATTATAA-AA-AT
1 ATAAAAAATTATAATAAGAT
*
2995 ATAAAAAATTCTAATAAGAT
1 ATAAAAAATTATAATAAGAT
3015 ATAAAA
1 ATAAAA
3021 GTTAGAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 13 0.57
19 2 0.09
20 8 0.35
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.27
Consensus pattern (20 bp):
ATAAAAAATTATAATAAGAT
Done.