Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008295.1 Hibiscus syriacus cultivar Beakdansim tig00110962_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: 741301
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 5
Found at i:718814 original size:17 final size:18
Alignment explanation
Indices: 718777--718814 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
718767 TTTTTTTTAT
718777 ATATTATTAAATATAAAA
1 ATATTATTAAATATAAAA
718795 ATATT-TTAAA-ATAAATA
1 ATATTATTAAATATAAA-A
718812 ATA
1 ATA
718815 AAAATAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 5 0.26
17 9 0.47
18 5 0.26
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
ATATTATTAAATATAAAA
Found at i:724821 original size:224 final size:224
Alignment explanation
Indices: 724418--724888 Score: 917
Period size: 224 Copynumber: 2.1 Consensus size: 224
724408 ATGGTGATGA
*
724418 TAACT-AATGGATAGGAAAATAATGAGTGGTTCTAAATTCAGTGGACAAGCAAAAAGCTTTCGTC
1 TAACTCAA-GGATTGGAAAATAATGAGTGGTTCTAAATTCAGTGGACAAGCAAAAAGCTTTCGTC
724482 TTAAATGGTGATTAAGACACACTGTAAACATGTGATTAACAATAATTAAGGTTTATCAGACATTG
65 TTAAATGGTGATTAAGACACACTGTAAACATGTGATTAACAATAATTAAGGTTTATCAGACATTG
724547 CATCATTTCAGCAAAACTCAATCATTAATGAGGTAGCAATTCAAATCGATCAATAAACAAGTCGG
130 CATCATTTCAGCAAAACTCAATCATTAATGAGGTAGCAATTCAAATCGATCAATAAACAAGTCGG
724612 GTTATATAATCCAATTTCAATTTGATTAAT
195 GTTATATAATCCAATTTCAATTTGATTAAT
724642 TAACTCAAGGATTGGAAAATAATGAGTGGTTCTAAATTCAGTGGACAAGCAAAAAGCTTTCGTCT
1 TAACTCAAGGATTGGAAAATAATGAGTGGTTCTAAATTCAGTGGACAAGCAAAAAGCTTTCGTCT
724707 TAAATGGTGATTAAGACACACTGTAAACATGTGATTAACAATAATTAAGGTTTATCAGACATTGC
66 TAAATGGTGATTAAGACACACTGTAAACATGTGATTAACAATAATTAAGGTTTATCAGACATTGC
724772 ATCATTTCAGCAAAACTCAATCATTAATGAGGTAGCAATTCAAATCGATCAATAAACAAGTCGGG
131 ATCATTTCAGCAAAACTCAATCATTAATGAGGTAGCAATTCAAATCGATCAATAAACAAGTCGGG
724837 TTATATAATCCAATTTCAATTTGATTAAT
196 TTATATAATCCAATTTCAATTTGATTAAT
724866 TAACTCAAGGATTGGAAAATAAT
1 TAACTCAAGGATTGGAAAATAAT
724889 TGAACAAGAA
Statistics
Matches: 245, Mismatches: 1, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
224 243 0.99
225 2 0.01
ACGTcount: A:0.40, C:0.14, G:0.16, T:0.30
Consensus pattern (224 bp):
TAACTCAAGGATTGGAAAATAATGAGTGGTTCTAAATTCAGTGGACAAGCAAAAAGCTTTCGTCT
TAAATGGTGATTAAGACACACTGTAAACATGTGATTAACAATAATTAAGGTTTATCAGACATTGC
ATCATTTCAGCAAAACTCAATCATTAATGAGGTAGCAATTCAAATCGATCAATAAACAAGTCGGG
TTATATAATCCAATTTCAATTTGATTAAT
Found at i:726115 original size:71 final size:71
Alignment explanation
Indices: 725999--726143 Score: 290
Period size: 71 Copynumber: 2.0 Consensus size: 71
725989 CCAGTGCACT
725999 AGGGAAACCAATCTCCATGGACTCTTTCACTGCTTCTAAAACTAGATTGCACTTTGCTAAAGTTT
1 AGGGAAACCAATCTCCATGGACTCTTTCACTGCTTCTAAAACTAGATTGCACTTTGCTAAAGTTT
726064 GTGTTG
66 GTGTTG
726070 AGGGAAACCAATCTCCATGGACTCTTTCACTGCTTCTAAAACTAGATTGCACTTTGCTAAAGTTT
1 AGGGAAACCAATCTCCATGGACTCTTTCACTGCTTCTAAAACTAGATTGCACTTTGCTAAAGTTT
726135 GTGTTG
66 GTGTTG
726141 AGG
1 AGG
726144 TTGATGTTAA
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 74 1.00
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.33
Consensus pattern (71 bp):
AGGGAAACCAATCTCCATGGACTCTTTCACTGCTTCTAAAACTAGATTGCACTTTGCTAAAGTTT
GTGTTG
Found at i:731841 original size:19 final size:21
Alignment explanation
Indices: 731817--731858 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
731807 TTCATAAAAG
731817 ATACAC-TAA-AAAAAGGAAT
1 ATACACTTAACAAAAAGGAAT
731836 ATACACTTAATCAAAAAGGAAT
1 ATACACTTAA-CAAAAAGGAAT
731858 A
1 A
731859 CATACACAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 6 0.30
20 3 0.15
22 11 0.55
ACGTcount: A:0.60, C:0.12, G:0.10, T:0.19
Consensus pattern (21 bp):
ATACACTTAACAAAAAGGAAT
Found at i:732825 original size:31 final size:31
Alignment explanation
Indices: 732790--732854 Score: 112
Period size: 31 Copynumber: 2.1 Consensus size: 31
732780 TCAACCGTTA
*
732790 AAATTATCAGTTTTGGTCAGTTTTAGTACCT
1 AAATTATCAGTTTTGGTCAGTTTTAATACCT
*
732821 AAATTATCAGTTTTGGTCGGTTTTAATACCT
1 AAATTATCAGTTTTGGTCAGTTTTAATACCT
732852 AAA
1 AAA
732855 CTTTTAACTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.29, C:0.12, G:0.15, T:0.43
Consensus pattern (31 bp):
AAATTATCAGTTTTGGTCAGTTTTAATACCT
Done.