Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010476.1 Kokia drynarioides strain JFW-HI SEQ_125376, 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: 6130
ACGTcount: A:0.36, C:0.15, G:0.12, T:0.37
Found at i:343 original size:29 final size:29
Alignment explanation
Indices: 299--480 Score: 172
Period size: 29 Copynumber: 6.2 Consensus size: 29
289 CTTAAATTGA
299 CAAAAATTCTTATTTTAACCCCAAAACTTT
1 CAAAAATTC-TATTTTAACCCCAAAACTTT
* **
329 CAAAAATTCTATTTTTACCCCCTAAC-TT
1 CAAAAATTCTATTTTAACCCCAAAACTTT
* * **
357 CTAAAAATCCCATTTTTAACCCTGAAACTTT
1 C-AAAAATTCTA-TTTTAACCCCAAAACTTT
* * ** *
388 CAAAAATTATATTTTTACCCCCGAACTTC
1 CAAAAATTCTATTTTAACCCCAAAACTTT
417 CAAAAA-TCTCATTTTAACCCCAAAACTTT
1 CAAAAATTCT-ATTTTAACCCCAAAACTTT
* * *
446 CAAAAATTATATTTTTACCCCTAAA-TTT
1 CAAAAATTCTATTTTAACCCCAAAACTTT
474 CAAAAAT
1 CAAAAAT
481 CCCATTTTGA
Statistics
Matches: 122, Mismatches: 25, Indels: 12
0.77 0.16 0.08
Matches are distributed among these distances:
28 15 0.12
29 75 0.61
30 29 0.24
31 3 0.02
ACGTcount: A:0.38, C:0.25, G:0.01, T:0.36
Consensus pattern (29 bp):
CAAAAATTCTATTTTAACCCCAAAACTTT
Found at i:460 original size:58 final size:58
Alignment explanation
Indices: 310--488 Score: 270
Period size: 59 Copynumber: 3.1 Consensus size: 58
300 AAAAATTCTT
* *
310 ATTTTAACCCCAAAACTTTCAAAAATTCTATTTTTACCCCCTAACTTCTAAAAATCCC
1 ATTTTAACCCCAAAACTTTCAAAAATTATATTTTTACCCCCTAACTTCCAAAAATCCC
** * *
368 ATTTTTAACCCTGAAACTTTCAAAAATTATATTTTTACCCCCGAACTTCCAAAAATCTC
1 A-TTTTAACCCCAAAACTTTCAAAAATTATATTTTTACCCCCTAACTTCCAAAAATCCC
* *
427 ATTTTAACCCCAAAACTTTCAAAAATTATATTTTTA-CCCCTAAATTTCAAAAATCCC
1 ATTTTAACCCCAAAACTTTCAAAAATTATATTTTTACCCCCTAACTTCCAAAAATCCC
484 ATTTT
1 ATTTT
489 GACCTCGAAT
Statistics
Matches: 108, Mismatches: 12, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
57 22 0.20
58 34 0.31
59 52 0.48
ACGTcount: A:0.37, C:0.26, G:0.01, T:0.36
Consensus pattern (58 bp):
ATTTTAACCCCAAAACTTTCAAAAATTATATTTTTACCCCCTAACTTCCAAAAATCCC
Found at i:552 original size:28 final size:29
Alignment explanation
Indices: 503--576 Score: 69
Period size: 28 Copynumber: 2.6 Consensus size: 29
493 TCGAATTTTC
* *
503 CCAAAATTATCGTTTCA-CCCCCAAGAAT
1 CCAAAATTATCATTTTACCCCCCAAGAAT
** *
531 CCAAAATTATCATTTTTGCCCCCGAGAAT
1 CCAAAATTATCATTTTACCCCCCAAGAAT
* *
560 CCGAAAAGTCTCATTTT
1 CC-AAAATTATCATTTT
577 GAACTCCGAT
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
28 14 0.37
29 12 0.32
30 12 0.32
ACGTcount: A:0.32, C:0.28, G:0.09, T:0.30
Consensus pattern (29 bp):
CCAAAATTATCATTTTACCCCCCAAGAAT
Found at i:577 original size:29 final size:29
Alignment explanation
Indices: 520--576 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
510 TATCGTTTCA
*
520 CCCCCAAGAATCCAAAATTATCATTTTTG
1 CCCCCAAGAATCCAAAAGTATCATTTTTG
* *
549 CCCCCGAGAATCCGAAAAGTCTCATTTT
1 CCCCCAAGAATCC-AAAAGTATCATTTT
577 GAACTCCGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 12 0.50
30 12 0.50
ACGTcount: A:0.32, C:0.30, G:0.11, T:0.28
Consensus pattern (29 bp):
CCCCCAAGAATCCAAAAGTATCATTTTTG
Found at i:2270 original size:19 final size:19
Alignment explanation
Indices: 2209--2272 Score: 64
Period size: 20 Copynumber: 3.4 Consensus size: 19
2199 TTATAATTAA
2209 ATTTAAA-TAAAAATA-TT
1 ATTTAAATTAAAAATATTT
2226 A-TT-AATATATAAAATATTT
1 ATTTAAAT-TA-AAAATATTT
*
2245 GAATTAAATTAAAAATATTT
1 -ATTTAAATTAAAAATATTT
2265 ATTTAAAT
1 ATTTAAAT
2273 CCTATTTAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
15 2 0.05
16 2 0.05
17 3 0.08
18 6 0.15
19 9 0.23
20 10 0.26
21 4 0.10
22 3 0.08
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.44
Consensus pattern (19 bp):
ATTTAAATTAAAAATATTT
Found at i:4165 original size:10 final size:10
Alignment explanation
Indices: 4152--4176 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
4142 TTCATTAAAA
4152 AAAATTATTG
1 AAAATTATTG
4162 AAAATTATTG
1 AAAATTATTG
4172 AAAAT
1 AAAAT
4177 AAAAAATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.36
Consensus pattern (10 bp):
AAAATTATTG
Found at i:4252 original size:23 final size:23
Alignment explanation
Indices: 4208--4252 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
4198 AAAAAAATTC
* **
4208 AAAACAAAATTAAATATGTTTAA
1 AAAACAAAAATAAATAAATTTAA
*
4231 AAAATAAAAATAAATAAATTTA
1 AAAACAAAAATAAATAAATTTA
4253 GTCAATTTTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (23 bp):
AAAACAAAAATAAATAAATTTAA
Found at i:5082 original size:19 final size:19
Alignment explanation
Indices: 5021--5084 Score: 64
Period size: 20 Copynumber: 3.4 Consensus size: 19
5011 TTACAATTAA
5021 ATTTAAA-TAAAAATA-TT
1 ATTTAAATTAAAAATATTT
5038 A-TT-AATATATAAAATATTT
1 ATTTAAAT-TA-AAAATATTT
*
5057 GAATTAAATTAAAAATATTT
1 -ATTTAAATTAAAAATATTT
5077 ATTTAAAT
1 ATTTAAAT
5085 CCTATTTAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
15 2 0.05
16 2 0.05
17 3 0.08
18 6 0.15
19 9 0.23
20 10 0.26
21 4 0.10
22 3 0.08
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.44
Consensus pattern (19 bp):
ATTTAAATTAAAAATATTT
Done.