Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002059.1 Hibiscus syriacus cultivar Beakdansim tig00004194_pilon, 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: 50631
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Found at i:4760 original size:5 final size:5
Alignment explanation
Indices: 4752--4780 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
4742 TTCTTTTTTT
4752 TTTCC TTTCC TTTCC TTTCC TTTCC TTTC
1 TTTCC TTTCC TTTCC TTTCC TTTCC TTTC
4781 AAGGTTAGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (5 bp):
TTTCC
Found at i:5565 original size:27 final size:29
Alignment explanation
Indices: 5531--5586 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
5521 CTTGTATAAG
5531 CTTTAGGGC-TT-TATATTACATATATAT
1 CTTTAGGGCTTTATATATTACATATATAT
5558 CTTTAGGGCTTTATATATTACATATATAT
1 CTTTAGGGCTTTATATATTACATATATAT
5587 TGCTTTTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
27 9 0.33
28 2 0.07
29 16 0.59
ACGTcount: A:0.30, C:0.11, G:0.11, T:0.48
Consensus pattern (29 bp):
CTTTAGGGCTTTATATATTACATATATAT
Found at i:10782 original size:2 final size:2
Alignment explanation
Indices: 10775--10804 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
10765 ATGACTTGAC
10775 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
10805 GTATCATATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:15576 original size:15 final size:15
Alignment explanation
Indices: 15556--15591 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
15546 AAGGAATTAT
15556 TTTTATCTTTTTAAG
1 TTTTATCTTTTTAAG
15571 TTTTATCTTTTTAAG
1 TTTTATCTTTTTAAG
15586 TTTTAT
1 TTTTAT
15592 ATTCGAACAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.19, C:0.06, G:0.06, T:0.69
Consensus pattern (15 bp):
TTTTATCTTTTTAAG
Found at i:16280 original size:2 final size:2
Alignment explanation
Indices: 16273--16302 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
16263 TTATTTATCG
16273 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16303 TTGCTTACAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:30787 original size:33 final size:33
Alignment explanation
Indices: 30742--30810 Score: 122
Period size: 33 Copynumber: 2.1 Consensus size: 33
30732 TTATGATGGG
30742 TTTTGATCCGATTTGATAGTTTACAATGAATTT
1 TTTTGATCCGATTTGATAGTTTACAATGAATTT
30775 TTTTGA-CTCGATTTGATAGTTTACAATGAATTT
1 TTTTGATC-CGATTTGATAGTTTACAATGAATTT
30808 TTT
1 TTT
30811 ATTTTAGAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
32 1 0.03
33 34 0.97
ACGTcount: A:0.26, C:0.09, G:0.14, T:0.51
Consensus pattern (33 bp):
TTTTGATCCGATTTGATAGTTTACAATGAATTT
Found at i:32627 original size:23 final size:23
Alignment explanation
Indices: 32597--32643 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
32587 ATCGATACTA
32597 TCCAAAATATCAGTACCATATAG
1 TCCAAAATATCAGTACCATATAG
32620 TCCAAAATATCAGTACCATATAG
1 TCCAAAATATCAGTACCATATAG
32643 T
1 T
32644 TGAAGATAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.43, C:0.21, G:0.09, T:0.28
Consensus pattern (23 bp):
TCCAAAATATCAGTACCATATAG
Found at i:33216 original size:19 final size:20
Alignment explanation
Indices: 33194--33234 Score: 66
Period size: 19 Copynumber: 2.1 Consensus size: 20
33184 ATATAGAAAT
*
33194 TTTATTTTTAAATTT-TTAA
1 TTTATATTTAAATTTATTAA
33213 TTTATATTTAAATTTATTAA
1 TTTATATTTAAATTTATTAA
33233 TT
1 TT
33235 AAAGAATCAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (20 bp):
TTTATATTTAAATTTATTAA
Found at i:33237 original size:32 final size:33
Alignment explanation
Indices: 33174--33237 Score: 78
Period size: 32 Copynumber: 2.0 Consensus size: 33
33164 ATTATTTCTA
*
33174 TTTTAATATTATATAGAAATTTTATTTTTAAAT
1 TTTTAATATTATATAGAAATTTTATTATTAAAT
**
33207 TTTTAAT-TTATATTTAAA-TTTATTAATTAAA
1 TTTTAATATTATATAGAAATTTTATT-ATTAAA
33238 GAATCAGGGT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
31 6 0.22
32 14 0.52
33 7 0.26
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.58
Consensus pattern (33 bp):
TTTTAATATTATATAGAAATTTTATTATTAAAT
Found at i:36825 original size:64 final size:64
Alignment explanation
Indices: 36700--36826 Score: 141
Period size: 64 Copynumber: 2.0 Consensus size: 64
36690 TCGAGTGACC
* * * *
36700 ATTTTGTAACTTTTAATAGTCAAAGAATTTAACAAAGCAACATCTTATAGTCTAAAGATCATTA
1 ATTTTGTAACTTTTAATAGTCAAAGAACTTAACAAAACAACATCTTATAATCTAAAAATCATTA
* ** * *
36764 ATTTTTTAACTTTTAATAGTTGATGAACTTAAGAAAACAACA-CTTTATAATC-AATAAATCATT
1 ATTTTGTAACTTTTAATAGTCAAAGAACTTAACAAAACAACATC-TTATAATCTAA-AAATCATT
36827 CGTATACTTC
Statistics
Matches: 52, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
63 3 0.06
64 49 0.94
ACGTcount: A:0.43, C:0.12, G:0.08, T:0.38
Consensus pattern (64 bp):
ATTTTGTAACTTTTAATAGTCAAAGAACTTAACAAAACAACATCTTATAATCTAAAAATCATTA
Found at i:49671 original size:14 final size:14
Alignment explanation
Indices: 49652--49679 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
49642 GTCGTGGTTG
49652 GCCAAAACAAAGAT
1 GCCAAAACAAAGAT
49666 GCCAAAACAAAGAT
1 GCCAAAACAAAGAT
49680 AAAGAGGTTG
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:0.57, C:0.21, G:0.14, T:0.07
Consensus pattern (14 bp):
GCCAAAACAAAGAT
Done.