Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003481.1 Hibiscus syriacus cultivar Beakdansim tig00007355_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: 64491
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:7564 original size:74 final size:76
Alignment explanation
Indices: 7472--7622 Score: 234
Period size: 78 Copynumber: 2.0 Consensus size: 76
7462 TGTAACATAG
* * *
7472 ATATATATAATAATTCTTT-TAAA-AAAATATGGCTAATTAACAAAATTTTATAAACATGGATGA
1 ATATATATAATAATTCTTTAAAAACAAAATATAGCTAATTAACAAAATTTAATAAACATGGATGA
7535 CTCAAAACGTT
66 CTCAAAACGTT
*
7546 ATATATATAATAATTCTTTAAAAAAACAAAATATAGCTAATTAACAAAATTTAATAAGCATGGAT
1 ATATATATAATAATTCTTT--AAAAACAAAATATAGCTAATTAACAAAATTTAATAAACATGGAT
7611 GACTCAAAACGT
64 GACTCAAAACGT
7623 AAATTACCCT
Statistics
Matches: 69, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
74 19 0.28
77 3 0.04
78 47 0.68
ACGTcount: A:0.50, C:0.10, G:0.08, T:0.32
Consensus pattern (76 bp):
ATATATATAATAATTCTTTAAAAACAAAATATAGCTAATTAACAAAATTTAATAAACATGGATGA
CTCAAAACGTT
Found at i:14612 original size:2 final size:2
Alignment explanation
Indices: 14605--14653 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
14595 ATTTGTTGAG
14605 TA TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA TA
14647 TA TA TA T
1 TA TA TA T
14654 TGGTATAACC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:14838 original size:2 final size:2
Alignment explanation
Indices: 14831--14883 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
14821 ATTGGTAGAG
14831 TA TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA TA
14873 TA TA TA TA TA T
1 TA TA TA TA TA T
14884 CAATTAGGGA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:35353 original size:16 final size:19
Alignment explanation
Indices: 35334--35368 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
35324 TTAGGTGGTG
35334 AAAA-TATATTTT-TAATA
1 AAAATTATATTTTATAATA
35351 AAAATTATATTTTATAAT
1 AAAATTATATTTTATAAT
35369 TTAAATTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 8 0.50
19 4 0.25
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
AAAATTATATTTTATAATA
Found at i:62044 original size:5 final size:5
Alignment explanation
Indices: 62034--62061 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
62024 GTTACGCCCA
62034 CGACC CGACC CGACC CGACC CGACC CGA
1 CGACC CGACC CGACC CGACC CGACC CGA
62062 GACGGACGGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.21, C:0.57, G:0.21, T:0.00
Consensus pattern (5 bp):
CGACC
Found at i:62712 original size:42 final size:42
Alignment explanation
Indices: 62664--62761 Score: 133
Period size: 42 Copynumber: 2.3 Consensus size: 42
62654 ATGAATTTGG
*
62664 AATAAATCGCAACGTGAACTTCGACTATCACAACGAACTTGA
1 AATAAATCGCAACGCGAACTTCGACTATCACAACGAACTTGA
* * * * * *
62706 AATAAATCGTAACGCGAACTTGGATTATCGCAACGAATTTGG
1 AATAAATCGCAACGCGAACTTCGACTATCACAACGAACTTGA
62748 AATAAATCGCAACG
1 AATAAATCGCAACG
62762 AATTTGGAAT
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 48 1.00
ACGTcount: A:0.40, C:0.20, G:0.17, T:0.22
Consensus pattern (42 bp):
AATAAATCGCAACGCGAACTTCGACTATCACAACGAACTTGA
Found at i:62756 original size:21 final size:20
Alignment explanation
Indices: 62660--62781 Score: 86
Period size: 21 Copynumber: 5.8 Consensus size: 20
62650 TCGCATGAAT
62660 TTGGAATAAATCGCAACGTGAAC
1 TTGGAAT-AATCGCAAC--GAAC
* * *
62683 TTCGACT-ATCACAACGAAC
1 TTGGAATAATCGCAACGAAC
* *
62702 TTGAAATAAATCGTAACGCGAAC
1 TTGGAAT-AATCGCAA--CGAAC
* *
62725 TTGG-ATTATCGCAACGAAT
1 TTGGAATAATCGCAACGAAC
*
62744 TTGGAATAAATCGCAACGAAT
1 TTGGAAT-AATCGCAACGAAC
*
62765 TTGGAATAATCACAACG
1 TTGGAATAATCGCAACG
62782 CGAACTTCGA
Statistics
Matches: 79, Mismatches: 14, Indels: 15
0.73 0.13 0.14
Matches are distributed among these distances:
19 16 0.20
20 11 0.14
21 37 0.47
22 2 0.03
23 13 0.16
ACGTcount: A:0.39, C:0.19, G:0.18, T:0.24
Consensus pattern (20 bp):
TTGGAATAATCGCAACGAAC
Done.