Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012973.1 Kokia drynarioides strain JFW-HI SEQ_127991, 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: 21156
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Warning! 90 characters in sequence are not A, C, G, or T
Found at i:2640 original size:53 final size:53
Alignment explanation
Indices: 2555--2676 Score: 217
Period size: 53 Copynumber: 2.3 Consensus size: 53
2545 ATTCTCCCTA
*
2555 TTTAGAGTATAATTTGTTCTCTTTGTATTATGTTTAACATGCATTTTTAGCAT
1 TTTATAGTATAATTTGTTCTCTTTGTATTATGTTTAACATGCATTTTTAGCAT
2608 TTTATAGTATAATTTGTTCTCTTTGTATTATGTTTAACATGCATTTTTAGCAT
1 TTTATAGTATAATTTGTTCTCTTTGTATTATGTTTAACATGCATTTTTAGCAT
2661 TTTATATGTAATAATT
1 TTTATA-GT-ATAATT
2677 GCATTTTCTA
Statistics
Matches: 66, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
53 58 0.88
54 2 0.03
55 6 0.09
ACGTcount: A:0.26, C:0.08, G:0.11, T:0.54
Consensus pattern (53 bp):
TTTATAGTATAATTTGTTCTCTTTGTATTATGTTTAACATGCATTTTTAGCAT
Found at i:5214 original size:20 final size:20
Alignment explanation
Indices: 5189--5232 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
5179 TTTAAAAGAC
5189 TAGATATCATTCAAAACTCA
1 TAGATATCATTCAAAACTCA
5209 TAGATATCATTCAAAACTCA
1 TAGATATCATTCAAAACTCA
5229 TAGA
1 TAGA
5233 AAGTTGATTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.45, C:0.18, G:0.07, T:0.30
Consensus pattern (20 bp):
TAGATATCATTCAAAACTCA
Found at i:12335 original size:15 final size:15
Alignment explanation
Indices: 12315--12350 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
12305 TTTACATTTT
*
12315 CTTTTATTTGTTTCA
1 CTTTTACTTGTTTCA
12330 CTTTTACTTGTTTCA
1 CTTTTACTTGTTTCA
*
12345 TTTTTA
1 CTTTTA
12351 AATTCTATGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.14, C:0.14, G:0.06, T:0.67
Consensus pattern (15 bp):
CTTTTACTTGTTTCA
Found at i:15327 original size:19 final size:19
Alignment explanation
Indices: 15303--15350 Score: 78
Period size: 19 Copynumber: 2.5 Consensus size: 19
15293 TAAAAATTGT
*
15303 GAAAGAGAAAAAGAGAAGA
1 GAAAGAGAAAAAGAGAAAA
15322 GAAAGAGAAAAAGAGAAAA
1 GAAAGAGAAAAAGAGAAAA
*
15341 GAAAAAGAAA
1 GAAAGAGAAA
15351 TATTGCTATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (19 bp):
GAAAGAGAAAAAGAGAAAA
Found at i:15343 original size:13 final size:13
Alignment explanation
Indices: 15304--15348 Score: 56
Period size: 13 Copynumber: 3.4 Consensus size: 13
15294 AAAAATTGTG
15304 AAAGAGAAAA-AGA
1 AAAGAGAAAAGA-A
*
15317 GAAGAGAAAGAGAA
1 AAAGAGAAA-AGAA
15331 AAAGAGAAAAGAA
1 AAAGAGAAAAGAA
15344 AAAGA
1 AAAGA
15349 AATATTGCTA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 17 0.61
14 10 0.36
15 1 0.04
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (13 bp):
AAAGAGAAAAGAA
Done.