Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007159.1 Hibiscus syriacus cultivar Beakdansim tig00018745_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: 49830
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Found at i:3609 original size:15 final size:15
Alignment explanation
Indices: 3589--3622 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
3579 GTAAAATACT
*
3589 AATTAATATATTAAA
1 AATTAATAGATTAAA
*
3604 AATTAATAGATTAAT
1 AATTAATAGATTAAA
3619 AATT
1 AATT
3623 CATCATCTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (15 bp):
AATTAATAGATTAAA
Found at i:15773 original size:29 final size:29
Alignment explanation
Indices: 15731--15793 Score: 108
Period size: 29 Copynumber: 2.2 Consensus size: 29
15721 AAATTTTACA
*
15731 GGCATGATAATAGAAAACACCCCGATAAT
1 GGCATGATAATAGAAAACACCCCGATAAC
*
15760 GGCATGATAATAGAAAACACCCTGATAAC
1 GGCATGATAATAGAAAACACCCCGATAAC
15789 GGCAT
1 GGCAT
15794 ATTGCATTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.43, C:0.21, G:0.19, T:0.17
Consensus pattern (29 bp):
GGCATGATAATAGAAAACACCCCGATAAC
Found at i:30086 original size:20 final size:20
Alignment explanation
Indices: 30044--30087 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
30034 TTTTCATTAA
*
30044 AAAAACAACATAATTAAATC
1 AAAAACAACATAATTAAAAC
*
30064 AAAAACAACA-ATTTAAAAAC
1 AAAAACAACATAATT-AAAAC
30084 AAAA
1 AAAA
30088 TATTTTTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 3 0.14
20 18 0.86
ACGTcount: A:0.70, C:0.14, G:0.00, T:0.16
Consensus pattern (20 bp):
AAAAACAACATAATTAAAAC
Found at i:33748 original size:64 final size:64
Alignment explanation
Indices: 33680--33903 Score: 249
Period size: 64 Copynumber: 3.5 Consensus size: 64
33670 TTTATGAATG
* **
33680 TGCATCGATGCATTGGTAGTGCATCGATGCA-CTCTTTTAA-AATAAATACATCGAATGCAATTC
1 TGCATCGATGCATAGGTAGTGCATCGATGCATC-CCATTAATAATAAA-ACATCGAATGCAATTC
33743 A
64 A
* * **
33744 TGCATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATGAAACATCGAATGCAATTGG
1 TGCATCGATGCATAGGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTCA
* ** * * * *
33808 TGCATCGATGCATAAGG-AGTGCATTGATGCATCCCAGCAATAATACAACATCGAATACACTTTA
1 TGCATCGATGCAT-AGGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTCA
*
33872 TGCACCGATGCATCA-GTAGTGCATCGATGCAT
1 TGCATCGATGCAT-AGGTAGTGCATCGATGCAT
33904 ACCTTCATTA
Statistics
Matches: 136, Mismatches: 20, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
63 1 0.01
64 127 0.93
65 8 0.06
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.27
Consensus pattern (64 bp):
TGCATCGATGCATAGGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTCA
Found at i:34356 original size:164 final size:164
Alignment explanation
Indices: 34085--34414 Score: 660
Period size: 164 Copynumber: 2.0 Consensus size: 164
34075 GTGCAATTTA
34085 ATTTGTACTTATATTATTGAACAAACATTTGGCTTGCGATGAGCCAGTGATGGAGTTACTATGGT
1 ATTTGTACTTATATTATTGAACAAACATTTGGCTTGCGATGAGCCAGTGATGGAGTTACTATGGT
34150 AAGAAGTAACTCCTAAAATGTTATTTGATTGGTGATCAATGTTATGATTTGTGTGATTATGAGAT
66 AAGAAGTAACTCCTAAAATGTTATTTGATTGGTGATCAATGTTATGATTTGTGTGATTATGAGAT
34215 ATATAAGTTATATGGAAAGTATATGTGAAATAAG
131 ATATAAGTTATATGGAAAGTATATGTGAAATAAG
34249 ATTTGTACTTATATTATTGAACAAACATTTGGCTTGCGATGAGCCAGTGATGGAGTTACTATGGT
1 ATTTGTACTTATATTATTGAACAAACATTTGGCTTGCGATGAGCCAGTGATGGAGTTACTATGGT
34314 AAGAAGTAACTCCTAAAATGTTATTTGATTGGTGATCAATGTTATGATTTGTGTGATTATGAGAT
66 AAGAAGTAACTCCTAAAATGTTATTTGATTGGTGATCAATGTTATGATTTGTGTGATTATGAGAT
34379 ATATAAGTTATATGGAAAGTATATGTGAAATAAG
131 ATATAAGTTATATGGAAAGTATATGTGAAATAAG
34413 AT
1 AT
34415 ATGAGCTTAT
Statistics
Matches: 166, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
164 166 1.00
ACGTcount: A:0.34, C:0.07, G:0.22, T:0.37
Consensus pattern (164 bp):
ATTTGTACTTATATTATTGAACAAACATTTGGCTTGCGATGAGCCAGTGATGGAGTTACTATGGT
AAGAAGTAACTCCTAAAATGTTATTTGATTGGTGATCAATGTTATGATTTGTGTGATTATGAGAT
ATATAAGTTATATGGAAAGTATATGTGAAATAAG
Found at i:34762 original size:31 final size:31
Alignment explanation
Indices: 34724--34976 Score: 461
Period size: 31 Copynumber: 8.2 Consensus size: 31
34714 AGAGTCGAGG
34724 GTTTACATATGTTTAAAGGCACATATGAACA
1 GTTTACATATGTTTAAAGGCACATATGAACA
*
34755 GTTTACATATGCTTAAAGGCACATATGAACA
1 GTTTACATATGTTTAAAGGCACATATGAACA
34786 GTTTACATATGTTTAAAGGCACATATGAACA
1 GTTTACATATGTTTAAAGGCACATATGAACA
* *
34817 GTTTACATATTTTTAAAGGCACATATGAATA
1 GTTTACATATGTTTAAAGGCACATATGAACA
34848 GTTTACATATGTTTAAAGGCACATATGAACA
1 GTTTACATATGTTTAAAGGCACATATGAACA
*
34879 GTTTACATATGTTTAAAGGCACATATGAAAA
1 GTTTACATATGTTTAAAGGCACATATGAACA
*
34910 GTTTATATATGTTTAAAGGCACATATGAACA
1 GTTTACATATGTTTAAAGGCACATATGAACA
34941 GTTTACATATGTTTAAAGGCACATATGAACA
1 GTTTACATATGTTTAAAGGCACATATGAACA
34972 GTTTA
1 GTTTA
34977 TATTATGACC
Statistics
Matches: 212, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 212 1.00
ACGTcount: A:0.39, C:0.12, G:0.16, T:0.34
Consensus pattern (31 bp):
GTTTACATATGTTTAAAGGCACATATGAACA
Found at i:37733 original size:64 final size:64
Alignment explanation
Indices: 37665--37888 Score: 242
Period size: 64 Copynumber: 3.5 Consensus size: 64
37655 TTTATGAATG
* **
37665 TGCATCGATGCATTGGTAGTGCATCGATGCA-CTCTTTTAA-AATAAATACATCGAATGCAATTC
1 TGCATCGATGCATAGGTAGTGCATCGATGCATC-CCATTAATAATAAA-ACATCGAATGCAATTC
37728 A
64 A
* * **
37729 TGCATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATGAAACATCGAATGCAATTGG
1 TGCATCGATGCATAGGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTCA
** * * * *
37793 TGCATCGATGCATAAGG-AGTGCATCGATGCATCCCAGCAATAATACAACATCGAATACATTTTA
1 TGCATCGATGCAT-AGGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTCA
*
37857 TTCA-CTGATGCATCA-GTAGTGCATCGATGCAT
1 TGCATC-GATGCAT-AGGTAGTGCATCGATGCAT
37889 AACTTCATTA
Statistics
Matches: 137, Mismatches: 18, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
63 2 0.01
64 127 0.93
65 8 0.06
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Consensus pattern (64 bp):
TGCATCGATGCATAGGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTCA
Found at i:38187 original size:19 final size:20
Alignment explanation
Indices: 38151--38188 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
38141 TAACTCCTAA
38151 AATGTTATTGATTGGTGATC
1 AATGTTATTGATTGGTGATC
*
38171 AATGTTA-TGATTTGTGAT
1 AATGTTATTGATTGGTGAT
38189 TATGAATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.26, C:0.03, G:0.24, T:0.47
Consensus pattern (20 bp):
AATGTTATTGATTGGTGATC
Found at i:38579 original size:31 final size:31
Alignment explanation
Indices: 38541--38724 Score: 350
Period size: 31 Copynumber: 5.9 Consensus size: 31
38531 AGAGTCGAGG
38541 GTTTACATATGTTTAAAGGCACATATGAACA
1 GTTTACATATGTTTAAAGGCACATATGAACA
38572 GTTTACATATGTTTAAAGGCACATATGAACA
1 GTTTACATATGTTTAAAGGCACATATGAACA
38603 GTTTACATATGTTTAAAGGCACATATGAACA
1 GTTTACATATGTTTAAAGGCACATATGAACA
* *
38634 GTTTACATATTTTTAAAGGCACATATGAATA
1 GTTTACATATGTTTAAAGGCACATATGAACA
38665 GTTTACATATGTTTAAAGGCACATATGAACA
1 GTTTACATATGTTTAAAGGCACATATGAACA
38696 GTTTACATATGTTTAAAGGCACATATGAA
1 GTTTACATATGTTTAAAGGCACATATGAA
38725 TTGTAATGTA
Statistics
Matches: 149, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 149 1.00
ACGTcount: A:0.39, C:0.12, G:0.16, T:0.34
Consensus pattern (31 bp):
GTTTACATATGTTTAAAGGCACATATGAACA
Found at i:39912 original size:3 final size:3
Alignment explanation
Indices: 39906--39971 Score: 80
Period size: 3 Copynumber: 22.0 Consensus size: 3
39896 ATTAATTTTT
* *
39906 TTA TTA TTA TTA TTTA TT- TTA TTA TTA TTA TTT TTA TTA ATA TTA
1 TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
39951 GTA TTA CTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA
39972 AATAAAAAAT
Statistics
Matches: 53, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
2 2 0.04
3 48 0.91
4 3 0.06
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:49016 original size:78 final size:81
Alignment explanation
Indices: 48816--49082 Score: 442
Period size: 80 Copynumber: 3.4 Consensus size: 81
48806 ATACTCATAG
48816 CTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTGGTAAAACCAATCATTGAATTTGAGATG
1 CTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAATCATTGAATTTGAGATG
*
48880 AATGTGTTCATAGCAT
66 AATGTGATCATAGCAT
48896 CTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAATCATTGAA-TTGAGATG
1 CTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAATCATTGAATTTGAGATG
48960 AATGTGATCATAGCAT
66 AATGTGATCATAGCAT
48976 CTTC-GGAAGTGTTC-TTGAGTTATCTGATCTGGTTTGGTAAAACCAATCATTGAATTTGAAAGA
1 CTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAATCATTGAATTTG--AGA
49039 TGAATGTGATCATAGCA-
64 TGAATGTGATCATAGCAT
*
49056 --TCTGAAAGTGTTCTTTGA-TTATCTGAT
1 CTTCTGGAAGTGTTCTTTGAGTTATCTGAT
49083 TTGGGTTGAT
Statistics
Matches: 179, Mismatches: 2, Indels: 13
0.92 0.01 0.07
Matches are distributed among these distances:
78 42 0.23
79 31 0.17
80 65 0.36
81 41 0.23
ACGTcount: A:0.27, C:0.12, G:0.22, T:0.38
Consensus pattern (81 bp):
CTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAATCATTGAATTTGAGATG
AATGTGATCATAGCAT
Done.