Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000155.1 Kokia drynarioides strain JFW-HI SEQ_110817, 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: 3691
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Found at i:717 original size:18 final size:17
Alignment explanation
Indices: 696--787 Score: 75
Period size: 18 Copynumber: 5.2 Consensus size: 17
686 AAATTCATAA
696 TAAATTTAAACTTAAATT
1 TAAATTTAAAC-TAAATT
714 TAAATTTTTAAAC-AAATT
1 TAAA--TTTAAACTAAATT
*
732 T-AATCTTAAAATAAATT
1 TAAAT-TTAAACTAAATT
749 TAAATTTTTAAAC-AAATT
1 TAAA--TTTAAACTAAATT
*
767 T-AATCTTAAAATAAATT
1 TAAAT-TTAAACTAAATT
784 TAAA
1 TAAA
788 GGGGAGTTTG
Statistics
Matches: 61, Mismatches: 3, Indels: 20
0.73 0.04 0.24
Matches are distributed among these distances:
15 2 0.03
16 10 0.16
17 16 0.26
18 20 0.33
19 5 0.08
20 8 0.13
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.42
Consensus pattern (17 bp):
TAAATTTAAACTAAATT
Found at i:749 original size:17 final size:17
Alignment explanation
Indices: 708--786 Score: 86
Period size: 17 Copynumber: 4.5 Consensus size: 17
698 AATTTAAACT
* *
708 TAAATTTAAATTTTTAAA
1 TAAATTT-AATCTTAAAA
*
726 CAAATTTAATCTTAAAA
1 TAAATTTAATCTTAAAA
* *
743 TAAATTTAAATTTTTAAA
1 TAAATTT-AATCTTAAAA
*
761 CAAATTTAATCTTAAAA
1 TAAATTTAATCTTAAAA
778 TAAATTTAA
1 TAAATTTAA
787 AGGGGAGTTT
Statistics
Matches: 50, Mismatches: 10, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
17 30 0.60
18 20 0.40
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (17 bp):
TAAATTTAATCTTAAAA
Found at i:752 original size:35 final size:35
Alignment explanation
Indices: 708--787 Score: 160
Period size: 35 Copynumber: 2.3 Consensus size: 35
698 AATTTAAACT
708 TAAATTTAAATTTTTAAACAAATTTAATCTTAAAA
1 TAAATTTAAATTTTTAAACAAATTTAATCTTAAAA
743 TAAATTTAAATTTTTAAACAAATTTAATCTTAAAA
1 TAAATTTAAATTTTTAAACAAATTTAATCTTAAAA
778 TAAATTTAAA
1 TAAATTTAAA
788 GGGGAGTTTG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 45 1.00
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (35 bp):
TAAATTTAAATTTTTAAACAAATTTAATCTTAAAA
Found at i:1346 original size:14 final size:14
Alignment explanation
Indices: 1327--1354 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1317 GTAAATTTAC
1327 AAAAAAATTAAATT
1 AAAAAAATTAAATT
1341 AAAAAAATTAAATT
1 AAAAAAATTAAATT
1355 TAGAAGACCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (14 bp):
AAAAAAATTAAATT
Found at i:1551 original size:34 final size:34
Alignment explanation
Indices: 1478--1552 Score: 91
Period size: 33 Copynumber: 2.2 Consensus size: 34
1468 TACTAAAAAC
*
1478 TTTTAATACTGTGAGATAGCATCTCATAGCACTT
1 TTTTAATACTGAGAGATAGCATCTCATAGCACTT
* *
1512 CTTTAATA-TGAGAGATAGCATCTCGTA-CTACGTT
1 TTTTAATACTGAGAGATAGCATCTCATAGC-AC-TT
1546 TTTTAAT
1 TTTTAAT
1553 GCGCCAATTT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
32 1 0.03
33 19 0.54
34 15 0.43
ACGTcount: A:0.29, C:0.16, G:0.15, T:0.40
Consensus pattern (34 bp):
TTTTAATACTGAGAGATAGCATCTCATAGCACTT
Found at i:1714 original size:18 final size:19
Alignment explanation
Indices: 1679--1715 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
1669 TTATTATAAA
*
1679 TATTTTAAATATAATTAAT
1 TATTTTAAATAGAATTAAT
1698 TATTTTAAA-AGAATTAAT
1 TATTTTAAATAGAATTAAT
1716 AATAAATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (19 bp):
TATTTTAAATAGAATTAAT
Done.