Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012910.1 Kokia drynarioides strain JFW-HI SEQ_127926, 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: 8134
ACGTcount: A:0.36, C:0.12, G:0.16, T:0.35
Warning! 50 characters in sequence are not A, C, G, or T
Found at i:2383 original size:15 final size:17
Alignment explanation
Indices: 2351--2398 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 17
2341 AAATATATAA
2351 TATTATATATAAACTTT
1 TATTATATATAAACTTT
*
2368 TATTATATGT-AA-TTT
1 TATTATATATAAACTTT
2383 TATT-TATA-AAA-TTT
1 TATTATATATAAACTTT
2397 TA
1 TA
2399 ATTTTATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
14 10 0.36
15 7 0.25
16 2 0.07
17 9 0.32
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (17 bp):
TATTATATATAAACTTT
Found at i:2385 original size:29 final size:29
Alignment explanation
Indices: 2343--2398 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
2333 TTTTGATCAA
*
2343 ATATATAATATTATATATAAACTTTTATT
1 ATATATAATATTATATATAAAATTTTATT
* * *
2372 ATATGTAATTTTATTTATAAAATTTTA
1 ATATATAATATTATATATAAAATTTTA
2399 ATTTTATTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (29 bp):
ATATATAATATTATATATAAAATTTTATT
Found at i:2627 original size:29 final size:27
Alignment explanation
Indices: 2552--2627 Score: 80
Period size: 31 Copynumber: 2.6 Consensus size: 27
2542 ACCATAATAA
2552 AAAATTATATGTATAATTACATCAAATT
1 AAAATT-TATGTATAATTACATCAAATT
* * *
2580 AAAATTTATATATTAAATTATTTATCGAATT
1 AAAATTTATGTA-T-AATTA--CATCAAATT
2611 AAAATTTATGTATAATT
1 AAAATTTATGTATAATT
2628 TTAATATTTA
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
27 5 0.12
28 7 0.17
29 9 0.22
30 1 0.03
31 18 0.45
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (27 bp):
AAAATTTATGTATAATTACATCAAATT
Found at i:4093 original size:44 final size:44
Alignment explanation
Indices: 4004--4091 Score: 106
Period size: 44 Copynumber: 2.0 Consensus size: 44
3994 TAGTGTCGAG
* * *
4004 TTAAGAGTTAGAATATGTGGTTAAAATAAGAAGATTAGGAAAAA
1 TTAAGAATTAGAATATGTAGTTAAAATAAGAAGATTAAGAAAAA
* *
4048 TTAAGAATTAGAATGTGTAGTCT-AAATAAGAAAGGTTAAGAAAA
1 TTAAGAATTAGAATATGTAGT-TAAAATAAG-AAGATTAAGAAAA
4092 TTCAAGGATT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
44 25 0.68
45 12 0.32
ACGTcount: A:0.50, C:0.01, G:0.22, T:0.27
Consensus pattern (44 bp):
TTAAGAATTAGAATATGTAGTTAAAATAAGAAGATTAAGAAAAA
Found at i:5890 original size:6 final size:6
Alignment explanation
Indices: 5879--5907 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
5869 ATTAATGTAA
5879 AAAAAG AAAAAG AAAAAG AAAAAG AAAAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAA
5908 TTGAATAGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:7858 original size:72 final size:72
Alignment explanation
Indices: 7770--7913 Score: 261
Period size: 72 Copynumber: 2.0 Consensus size: 72
7760 CATCCCATTG
*
7770 GATGTGTCCCTCTGGATGTGGTTTATGCCAACCGTCTCTTACGACACCAAAAGTTCTCAACATGG
1 GATGTGTCCCTCTGGATGTGGTTTATGCCAACAGTCTCTTACGACACCAAAAGTTCTCAACATGG
7835 AAAATTT
66 AAAATTT
*
7842 GATGTGTCCCTCTGGATGTGGTTTATGCCAACAGTCTCTTGCGACACCAAAAGTTCTCAACATGG
1 GATGTGTCCCTCTGGATGTGGTTTATGCCAACAGTCTCTTACGACACCAAAAGTTCTCAACATGG
*
7907 GAAATTT
66 AAAATTT
7914 AGACACATTG
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
72 69 1.00
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.31
Consensus pattern (72 bp):
GATGTGTCCCTCTGGATGTGGTTTATGCCAACAGTCTCTTACGACACCAAAAGTTCTCAACATGG
AAAATTT
Done.