Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004805.1 Kokia drynarioides strain JFW-HI SEQ_118433, 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: 46439
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Warning! 141 characters in sequence are not A, C, G, or T
Found at i:3776 original size:22 final size:22
Alignment explanation
Indices: 3717--3776 Score: 61
Period size: 22 Copynumber: 2.8 Consensus size: 22
3707 AGCAACTTGC
*
3717 TACT-TTTTGCTGTTATTTTGT
1 TACTATTTTGCTGTTATATTGT
* *
3738 CACTGA-TTTGCTATTATATTGT
1 TACT-ATTTTGCTGTTATATTGT
*
3760 TACTATTTTGATGTTAT
1 TACTATTTTGCTGTTAT
3777 TATTTGGATA
Statistics
Matches: 30, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
21 4 0.13
22 26 0.87
ACGTcount: A:0.18, C:0.10, G:0.13, T:0.58
Consensus pattern (22 bp):
TACTATTTTGCTGTTATATTGT
Found at i:7245 original size:2 final size:2
Alignment explanation
Indices: 7238--7264 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
7228 TCCCTCCTTG
7238 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
7265 CAAGATTCTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:9578 original size:3 final size:3
Alignment explanation
Indices: 9570--9595 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
9560 GGTAAAAACA
9570 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
9596 AATCAACCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:19479 original size:2 final size:2
Alignment explanation
Indices: 19472--19505 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
19462 TATCAATTCC
19472 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
19506 ATATATATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:23884 original size:36 final size:38
Alignment explanation
Indices: 23840--23912 Score: 96
Period size: 40 Copynumber: 1.9 Consensus size: 38
23830 GATAGACCCA
*
23840 TCTAAGACAA-TCTT-AAAAAGATTGGGATAAATCTTG
1 TCTAAGACAATTCTTAAAAAAAATTGGGATAAATCTTG
*
23876 TCTAAGACAACTTTTTTAAAAAAAATTGGGATAAATC
1 TCTAAGACAA--TTCTTAAAAAAAATTGGGATAAATC
23913 CGTTAAAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
36 10 0.32
39 3 0.10
40 18 0.58
ACGTcount: A:0.44, C:0.11, G:0.14, T:0.32
Consensus pattern (38 bp):
TCTAAGACAATTCTTAAAAAAAATTGGGATAAATCTTG
Found at i:27452 original size:2 final size:2
Alignment explanation
Indices: 27445--27470 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
27435 ACGTACATTT
27445 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
27471 AGTTGTCATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:28373 original size:27 final size:30
Alignment explanation
Indices: 28332--28397 Score: 84
Period size: 28 Copynumber: 2.3 Consensus size: 30
28322 CAACTACGTT
* *
28332 AAAAAAAATGGAGAAG-GGA-GGAAAATAA
1 AAAAAAAATGCAGAAGAGAATGGAAAATAA
28360 AAAAAAAAT-CAGAAGAGAATGGAAAATAA
1 AAAAAAAATGCAGAAGAGAATGGAAAATAA
28389 AAGAAAAAA
1 AA-AAAAAA
28398 AATAAAGTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 5 0.15
28 11 0.33
29 11 0.33
30 6 0.18
ACGTcount: A:0.70, C:0.02, G:0.21, T:0.08
Consensus pattern (30 bp):
AAAAAAAATGCAGAAGAGAATGGAAAATAA
Found at i:28409 original size:20 final size:21
Alignment explanation
Indices: 28386--28424 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
28376 GAATGGAAAA
28386 TAAAAGAA-AAAAAATAAAGT
1 TAAAAGAACAAAAAATAAAGT
*
28406 TAAAAGAACATAAAATAAA
1 TAAAAGAACAAAAAATAAA
28425 ACAATTAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.74, C:0.03, G:0.08, T:0.15
Consensus pattern (21 bp):
TAAAAGAACAAAAAATAAAGT
Found at i:29427 original size:18 final size:18
Alignment explanation
Indices: 29404--29441 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
29394 GTCACTGTTG
29404 TTTGTTTCGGATTACATT
1 TTTGTTTCGGATTACATT
29422 TTTGTTTCGGATTACATT
1 TTTGTTTCGGATTACATT
29440 TT
1 TT
29442 AGTCATTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.16, C:0.11, G:0.16, T:0.58
Consensus pattern (18 bp):
TTTGTTTCGGATTACATT
Done.