Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003383.1 Kokia drynarioides strain JFW-HI SEQ_116117, 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: 50963
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 235 characters in sequence are not A, C, G, or T
Found at i:11738 original size:20 final size:19
Alignment explanation
Indices: 11713--11760 Score: 51
Period size: 20 Copynumber: 2.5 Consensus size: 19
11703 GTAAATATAA
11713 TTTTATTAAAATTTTAATAT
1 TTTTATTAAAATTTTAAT-T
* **
11733 TTTTATCAACCTTTTAATT
1 TTTTATTAAAATTTTAATT
*
11752 ATTTATTAA
1 TTTTATTAA
11761 TTTATTAATT
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
19 8 0.35
20 15 0.65
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.58
Consensus pattern (19 bp):
TTTTATTAAAATTTTAATT
Found at i:15759 original size:3 final size:3
Alignment explanation
Indices: 15751--15780 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
15741 TTTCTGAAAT
15751 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
15781 TCCATATTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:15869 original size:22 final size:22
Alignment explanation
Indices: 15814--15870 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 22
15804 TTTAAAATAC
15814 TGGATTTTCCCTGTTTGTTACCAA
1 TGGA-TTT-CCTGTTTGTTACCAA
*
15838 TGGGATTTCCTGTTTGTTACAGAA
1 T-GGATTTCCTGTTTGTTAC-CAA
15862 T-GATTTCCT
1 TGGATTTCCT
15871 TTTTAAAAAG
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
22 8 0.27
23 12 0.40
24 7 0.23
25 3 0.10
ACGTcount: A:0.18, C:0.18, G:0.19, T:0.46
Consensus pattern (22 bp):
TGGATTTCCTGTTTGTTACCAA
Found at i:20619 original size:17 final size:17
Alignment explanation
Indices: 20593--20634 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
20583 GTAGATATTT
20593 AGAG-AGAAAAAAAAAA
1 AGAGAAGAAAAAAAAAA
* *
20609 AGAGAAGAAAAGAAACA
1 AGAGAAGAAAAAAAAAA
*
20626 AGACAAGAA
1 AGAGAAGAA
20635 GCATGGAATC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
16 4 0.18
17 18 0.82
ACGTcount: A:0.74, C:0.05, G:0.21, T:0.00
Consensus pattern (17 bp):
AGAGAAGAAAAAAAAAA
Found at i:25384 original size:2 final size:2
Alignment explanation
Indices: 25372--25406 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
25362 CGTTCATAGG
*
25372 TA TA CA TA 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 TA TA TA TA T
25407 GGAAAAGATG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:32507 original size:2 final size:2
Alignment explanation
Indices: 32500--32528 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
32490 TGATTTGTTA
32500 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
32529 CATTTATAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:40485 original size:20 final size:21
Alignment explanation
Indices: 40451--40494 Score: 72
Period size: 20 Copynumber: 2.1 Consensus size: 21
40441 TTTAATGTAA
40451 AAATATTGATAACAATACATT
1 AAATATTGATAACAATACATT
*
40472 AAATATTG-TAACAATAGATT
1 AAATATTGATAACAATACATT
40492 AAA
1 AAA
40495 AGAAAATTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 14 0.64
21 8 0.36
ACGTcount: A:0.55, C:0.07, G:0.07, T:0.32
Consensus pattern (21 bp):
AAATATTGATAACAATACATT
Done.