Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008226.1 Hibiscus syriacus cultivar Beakdansim tig00110860_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: 835745
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 5
Found at i:782269 original size:30 final size:32
Alignment explanation
Indices: 782235--782293 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 32
782225 CCCAAGAACA
782235 TAGGTAA-T-TGTCCATATGTCCCAAAAGGCC
1 TAGGTAATTATGTCCATATGTCCCAAAAGGCC
**
782265 TAGGTAATTATGTTTATATGTCCCAAAAG
1 TAGGTAATTATGTCCATATGTCCCAAAAG
782294 ATATAGGTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 7 0.28
31 1 0.04
32 17 0.68
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Consensus pattern (32 bp):
TAGGTAATTATGTCCATATGTCCCAAAAGGCC
Found at i:782856 original size:12 final size:14
Alignment explanation
Indices: 782841--782872 Score: 50
Period size: 12 Copynumber: 2.4 Consensus size: 14
782831 GAGACTTACG
782841 AGGAGAAGAA-G-A
1 AGGAGAAGAATGCA
782853 AGGAGAAGAATGCA
1 AGGAGAAGAATGCA
782867 AGGAGA
1 AGGAGA
782873 TAAGTTTTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 10 0.56
13 1 0.06
14 7 0.39
ACGTcount: A:0.53, C:0.03, G:0.41, T:0.03
Consensus pattern (14 bp):
AGGAGAAGAATGCA
Found at i:784928 original size:24 final size:24
Alignment explanation
Indices: 784901--784952 Score: 95
Period size: 24 Copynumber: 2.2 Consensus size: 24
784891 TGGGGTGGTG
*
784901 GAAAGGAAACACATGCATATAGTA
1 GAAAGAAAACACATGCATATAGTA
784925 GAAAGAAAACACATGCATATAGTA
1 GAAAGAAAACACATGCATATAGTA
784949 GAAA
1 GAAA
784953 TTGCCTTAAC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.54, C:0.12, G:0.19, T:0.15
Consensus pattern (24 bp):
GAAAGAAAACACATGCATATAGTA
Found at i:796512 original size:12 final size:12
Alignment explanation
Indices: 796495--796528 Score: 68
Period size: 12 Copynumber: 2.8 Consensus size: 12
796485 CGAATATAAA
796495 TTGTAAAATCAT
1 TTGTAAAATCAT
796507 TTGTAAAATCAT
1 TTGTAAAATCAT
796519 TTGTAAAATC
1 TTGTAAAATC
796529 TTAAAATTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.41
Consensus pattern (12 bp):
TTGTAAAATCAT
Found at i:797304 original size:21 final size:21
Alignment explanation
Indices: 797280--797323 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
797270 GAGCTGGAGG
*
797280 AGGAGGAGCGCGAGAAGAACT
1 AGGAGCAGCGCGAGAAGAACT
* *
797301 AGGAGCAGCTCGTGAAGAACT
1 AGGAGCAGCGCGAGAAGAACT
797322 AG
1 AG
797324 CTCCCGGGGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.36, C:0.16, G:0.39, T:0.09
Consensus pattern (21 bp):
AGGAGCAGCGCGAGAAGAACT
Found at i:803181 original size:22 final size:21
Alignment explanation
Indices: 803139--803178 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
803129 GAGTTTGTTT
*
803139 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
803160 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
803179 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:805373 original size:20 final size:21
Alignment explanation
Indices: 805350--805389 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
805340 GAATCGAATA
805350 TAAAAT-TGTAAAA-TCATTTG
1 TAAAATCT-TAAAATTCATTTG
805370 TAAAATCTTAAAATTCATTT
1 TAAAATCTTAAAATTCATTT
805390 AACTTAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.42
Consensus pattern (21 bp):
TAAAATCTTAAAATTCATTTG
Found at i:809237 original size:35 final size:34
Alignment explanation
Indices: 809152--809238 Score: 88
Period size: 35 Copynumber: 2.5 Consensus size: 34
809142 ATTTGATATT
* *
809152 TAAATACAACAAACTTACAATAAGAATTGAATGG
1 TAAATACAACAAAATTACAATAAGAATTAAATGG
* *
809186 TAAATGATAACCAAATTACAATAACTGATATTAAATGG
1 TAAAT-ACAACAAAATTACAATAA--GA-ATTAAATGG
809224 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
809239 ACTAAAATAT
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
34 5 0.11
35 24 0.55
36 1 0.02
37 5 0.11
38 9 0.20
ACGTcount: A:0.54, C:0.10, G:0.09, T:0.26
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGAATTAAATGG
Found at i:812694 original size:24 final size:24
Alignment explanation
Indices: 812646--812694 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
812636 ATTATTAAAT
*
812646 TTATTATTAATTATAATAATAATA
1 TTATTATTAATTATAAAAATAATA
*
812670 TTATTATTAGTTA-AAAAATATATA
1 TTATTATTAATTATAAAAATA-ATA
812694 T
1 T
812695 AAATTTTAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 6 0.27
24 16 0.73
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (24 bp):
TTATTATTAATTATAAAAATAATA
Found at i:813613 original size:22 final size:22
Alignment explanation
Indices: 813587--813630 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
813577 AATTTAACAT
* *
813587 TATTTAGATATTACTTTTTAAA
1 TATTTAAATATAACTTTTTAAA
*
813609 TATTTAAATATAATTTTTTAAA
1 TATTTAAATATAACTTTTTAAA
813631 CATACATTCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (22 bp):
TATTTAAATATAACTTTTTAAA
Found at i:819837 original size:37 final size:37
Alignment explanation
Indices: 819783--819866 Score: 127
Period size: 37 Copynumber: 2.3 Consensus size: 37
819773 TGGTAATAAC
819783 TTTGAAAAA-ATGGTTTTCAAAGTTTGGTAAATGTTT
1 TTTGAAAAATATGGTTTTCAAAGTTTGGTAAATGTTT
*
819819 ATTTGAAAAATA-GTTTTTCAAAGTTTGGTAAATGTTT
1 -TTTGAAAAATATGGTTTTCAAAGTTTGGTAAATGTTT
*
819856 GTTGAAAAATA
1 TTTGAAAAATA
819867 ATAATGGGAT
Statistics
Matches: 44, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
36 10 0.23
37 33 0.75
38 1 0.02
ACGTcount: A:0.37, C:0.02, G:0.18, T:0.43
Consensus pattern (37 bp):
TTTGAAAAATATGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:831825 original size:22 final size:21
Alignment explanation
Indices: 831795--831835 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
831785 TGTAATTAGA
831795 AAAATTTATCAAGAGTAATCT
1 AAAATTTATCAAGAGTAATCT
**
831816 AAAATGTTATTTAGAGTAAT
1 AAAAT-TTATCAAGAGTAAT
831836 TTGAGTAACA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.46, C:0.05, G:0.12, T:0.37
Consensus pattern (21 bp):
AAAATTTATCAAGAGTAATCT
Found at i:833146 original size:15 final size:15
Alignment explanation
Indices: 833095--833147 Score: 54
Period size: 16 Copynumber: 3.5 Consensus size: 15
833085 AAAAAAATAA
*
833095 TTAATTAATAA-ATT
1 TTAATAAATAATATT
* *
833109 TAAATAAATAATAAT
1 TTAATAAATAATATT
*
833124 TTATATAAATATTATT
1 TTA-ATAAATAATATT
833140 TTAATAAA
1 TTAATAAA
833148 CAAATAATAT
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
14 9 0.29
15 9 0.29
16 13 0.42
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TTAATAAATAATATT
Found at i:834505 original size:17 final size:18
Alignment explanation
Indices: 834462--834506 Score: 83
Period size: 18 Copynumber: 2.6 Consensus size: 18
834452 AAATCAAATG
834462 GGTTAACACTTAAACTAA
1 GGTTAACACTTAAACTAA
834480 GGTTAACACTTAAACTAA
1 GGTTAACACTTAAACTAA
834498 GG-TAACACT
1 GGTTAACACT
834507 ACTCCGTTAC
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 7 0.26
18 20 0.74
ACGTcount: A:0.42, C:0.18, G:0.13, T:0.27
Consensus pattern (18 bp):
GGTTAACACTTAAACTAA
Done.