Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002156.1 Hibiscus syriacus cultivar Beakdansim tig00004403_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: 53146
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:9112 original size:39 final size:39
Alignment explanation
Indices: 9058--9141 Score: 168
Period size: 39 Copynumber: 2.2 Consensus size: 39
9048 GCCAGCAAAT
9058 GGTTACGATAGGGACCTTACTACAAACGATTAAAAGTTG
1 GGTTACGATAGGGACCTTACTACAAACGATTAAAAGTTG
9097 GGTTACGATAGGGACCTTACTACAAACGATTAAAAGTTG
1 GGTTACGATAGGGACCTTACTACAAACGATTAAAAGTTG
9136 GGTTAC
1 GGTTAC
9142 AAAATGATAG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 45 1.00
ACGTcount: A:0.35, C:0.15, G:0.24, T:0.26
Consensus pattern (39 bp):
GGTTACGATAGGGACCTTACTACAAACGATTAAAAGTTG
Found at i:9381 original size:19 final size:18
Alignment explanation
Indices: 9354--9390 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
9344 AAAAGTAACG
9354 ATAAAAATAAGAGAAAAAA
1 ATAAAAATAAGA-AAAAAA
*
9373 ATAAGAATAAGAAAAAAA
1 ATAAAAATAAGAAAAAAA
9391 TGTTTATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.78, C:0.00, G:0.11, T:0.11
Consensus pattern (18 bp):
ATAAAAATAAGAAAAAAA
Found at i:11478 original size:18 final size:19
Alignment explanation
Indices: 11429--11484 Score: 57
Period size: 18 Copynumber: 3.1 Consensus size: 19
11419 TAGATAATTT
11429 TTTTA-ATATTTTAATAAA
1 TTTTACATATTTTAATAAA
11447 TTTTACA-ATTTTTAAT-AA
1 TTTTACATA-TTTTAATAAA
*
11465 -TTTACATATGTTTAACAAA
1 TTTTACATAT-TTTAATAAA
11484 T
1 T
11485 CTATTTTTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 10
0.74 0.02 0.24
Matches are distributed among these distances:
17 7 0.23
18 14 0.45
19 10 0.32
ACGTcount: A:0.41, C:0.05, G:0.02, T:0.52
Consensus pattern (19 bp):
TTTTACATATTTTAATAAA
Found at i:30198 original size:25 final size:26
Alignment explanation
Indices: 30159--30220 Score: 74
Period size: 25 Copynumber: 2.5 Consensus size: 26
30149 AAGATAAAAA
* * * *
30159 AAATCATAATTATTTTCTTAATTAAT
1 AAATAATAATAATTTTATTAAATAAT
30185 -AATAATAATAATTTTATTAAATAAT
1 AAATAATAATAATTTTATTAAATAAT
30210 AAATAA-AATAA
1 AAATAATAATAA
30221 AATATATTAG
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
25 26 0.84
26 5 0.16
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (26 bp):
AAATAATAATAATTTTATTAAATAAT
Found at i:30728 original size:22 final size:22
Alignment explanation
Indices: 30687--30745 Score: 68
Period size: 21 Copynumber: 2.7 Consensus size: 22
30677 TCAAATGTGA
* *
30687 ATAAATAAAAAAATTAAAGAGACG
1 ATAAAGAAAAAAAAT-AA-AGACG
30711 A-AAAGAAAAAAAAT-AAGACG
1 ATAAAGAAAAAAAATAAAGACG
30731 ATAAAGAAAAAAAAT
1 ATAAAGAAAAAAAAT
30746 CAGGATAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
20 6 0.19
21 14 0.44
23 11 0.34
24 1 0.03
ACGTcount: A:0.73, C:0.03, G:0.12, T:0.12
Consensus pattern (22 bp):
ATAAAGAAAAAAAATAAAGACG
Found at i:30729 original size:20 final size:21
Alignment explanation
Indices: 30706--30745 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
30696 AAAATTAAAG
30706 AGACGA-AAAGAAAAAAAATA
1 AGACGATAAAGAAAAAAAATA
30726 AGACGATAAAGAAAAAAAAT
1 AGACGATAAAGAAAAAAAAT
30746 CAGGATAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.72, C:0.05, G:0.15, T:0.07
Consensus pattern (21 bp):
AGACGATAAAGAAAAAAAATA
Found at i:30752 original size:19 final size:20
Alignment explanation
Indices: 30712--30754 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
30702 AAAGAGACGA
30712 AAAGAAAAAAAATAAGACGAT
1 AAAGAAAAAAAATAAGA-GAT
*
30733 AAAGAAAAAAAATCAG-GAT
1 AAAGAAAAAAAATAAGAGAT
30752 AAA
1 AAA
30755 ATATGGGTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 6 0.29
21 15 0.71
ACGTcount: A:0.72, C:0.05, G:0.14, T:0.09
Consensus pattern (20 bp):
AAAGAAAAAAAATAAGAGAT
Found at i:34602 original size:29 final size:29
Alignment explanation
Indices: 34552--34628 Score: 109
Period size: 29 Copynumber: 2.6 Consensus size: 29
34542 TACGGTTCGG
* * *
34552 TTAATCGAACCAAAATTTATTTGAAAATTA
1 TTAACCGAACC-AAATTAATTTAAAAATTA
34582 TTAACCGAACCAAATTAATTTAAAAATTA
1 TTAACCGAACCAAATTAATTTAAAAATTA
*
34611 TTAACCGAACCGAATTAA
1 TTAACCGAACCAAATTAA
34629 CCGAATTAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
29 33 0.77
30 10 0.23
ACGTcount: A:0.48, C:0.14, G:0.06, T:0.31
Consensus pattern (29 bp):
TTAACCGAACCAAATTAATTTAAAAATTA
Found at i:34863 original size:29 final size:29
Alignment explanation
Indices: 34815--34884 Score: 95
Period size: 29 Copynumber: 2.4 Consensus size: 29
34805 CGGTTAATCG
* *
34815 AACCAAACTTTATTTAAAAATTATTAACTA
1 AACCAAA-TTAATTTAAAAATTATTAACAA
*
34845 AACCAAATTAATTTGAAAATTATTAACAA
1 AACCAAATTAATTTAAAAATTATTAACAA
*
34874 AACCGAATTAA
1 AACCAAATTAA
34885 CTGATTTTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
29 29 0.81
30 7 0.19
ACGTcount: A:0.53, C:0.13, G:0.03, T:0.31
Consensus pattern (29 bp):
AACCAAATTAATTTAAAAATTATTAACAA
Found at i:34959 original size:138 final size:139
Alignment explanation
Indices: 34631--35008 Score: 501
Period size: 138 Copynumber: 2.7 Consensus size: 139
34621 CGAATTAACC
* * * * *
34631 GAATTAATCGAAGCAAAAATTAGGATAACTCAGTTCGGTTAATCAAACCAAAATTTA-TTAGAAA
1 GAATTAATCGAAGCAAAAATTCGGTTAATTCGGTTCGGTTAATCGAACCAAAATTTATTTA-AAA
* * * ** *
34695 ATTATTAACCAACCCGAAA-TAATTTTAAAATTATTAACCGAATCGAATTAACCAATTTTTTTAA
65 ATTATTAACTAAACC-AAATTAATTTGAAAATTATTAACAAAACCGAATTAACCAATTTTTTTAA
34759 AATTATTAATT
129 AATTATTAATT
* *
34770 GAATTAATCGTAGCAAAAATTCGGTTAATTCGGTTCGGTTAATCGAACCAAACTTTATTTAAAAA
1 GAATTAATCGAAGCAAAAATTCGGTTAATTCGGTTCGGTTAATCGAACCAAAATTTATTTAAAAA
**
34835 TTATTAACTAAACCAAATTAATTTGAAAATTATTAACAAAACCGAATTAACTGATTTTTTT-AAA
66 TTATTAACTAAACCAAATTAATTTGAAAATTATTAACAAAACCGAATTAACCAATTTTTTTAAAA
34899 TTATTAATT
131 TTATTAATT
* * * * *
34908 GAATTATTTGAAGCAAAAACTCGGTTAATTCGGTTCGATTAATCGAACCAAAATTTATTTGAAAA
1 GAATTAATCGAAGCAAAAATTCGGTTAATTCGGTTCGGTTAATCGAACCAAAATTTATTTAAAAA
* * * *
34973 TTATTAATTGAATCGAATTAATTTGAAAATTATTAA
66 TTATTAACTAAACCAAATTAATTTGAAAATTATTAA
35009 TCGAACCGAA
Statistics
Matches: 211, Mismatches: 26, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
138 105 0.50
139 103 0.49
140 3 0.01
ACGTcount: A:0.43, C:0.11, G:0.10, T:0.35
Consensus pattern (139 bp):
GAATTAATCGAAGCAAAAATTCGGTTAATTCGGTTCGGTTAATCGAACCAAAATTTATTTAAAAA
TTATTAACTAAACCAAATTAATTTGAAAATTATTAACAAAACCGAATTAACCAATTTTTTTAAAA
TTATTAATT
Found at i:34996 original size:29 final size:29
Alignment explanation
Indices: 34945--35018 Score: 103
Period size: 29 Copynumber: 2.5 Consensus size: 29
34935 ATTCGGTTCG
* *
34945 ATTAATCGAACCAAAATTTATTTGAAAATT
1 ATTAATCGAACC-GAATTAATTTGAAAATT
* *
34975 ATTAATTGAATCGAATTAATTTGAAAATT
1 ATTAATCGAACCGAATTAATTTGAAAATT
35004 ATTAATCGAACCGAA
1 ATTAATCGAACCGAA
35019 CAAATTTCGA
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
29 28 0.74
30 10 0.26
ACGTcount: A:0.46, C:0.09, G:0.09, T:0.35
Consensus pattern (29 bp):
ATTAATCGAACCGAATTAATTTGAAAATT
Found at i:35024 original size:29 final size:29
Alignment explanation
Indices: 34964--35025 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 29
34954 ACCAAAATTT
* * **
34964 ATTTGAAAATTATTAATTGAATCGAATTA
1 ATTTGAAAATTATTAATCGAACCGAACAA
34993 ATTTGAAAATTATTAATCGAACCGAACAA
1 ATTTGAAAATTATTAATCGAACCGAACAA
35022 ATTT
1 ATTT
35026 CGATGAATTC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.45, C:0.08, G:0.10, T:0.37
Consensus pattern (29 bp):
ATTTGAAAATTATTAATCGAACCGAACAA
Found at i:40644 original size:14 final size:14
Alignment explanation
Indices: 40622--40654 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
40612 CCTCGCATAG
*
40622 CTCGTTCGGATGGC
1 CTCGGTCGGATGGC
40636 CTCGGTCGGATGGC
1 CTCGGTCGGATGGC
40650 CTCGG
1 CTCGG
40655 ATGCTCTCGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.06, C:0.30, G:0.39, T:0.24
Consensus pattern (14 bp):
CTCGGTCGGATGGC
Found at i:40654 original size:10 final size:10
Alignment explanation
Indices: 40641--40677 Score: 58
Period size: 10 Copynumber: 3.7 Consensus size: 10
40631 ATGGCCTCGG
40641 TCGGATGGCC
1 TCGGATGGCC
40651 TCGGAT-GCTC
1 TCGGATGGC-C
40661 TCGGATGGCC
1 TCGGATGGCC
40671 TCGGATG
1 TCGGATG
40678 CCCAGCGTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
9 2 0.08
10 21 0.84
11 2 0.08
ACGTcount: A:0.11, C:0.27, G:0.38, T:0.24
Consensus pattern (10 bp):
TCGGATGGCC
Found at i:40666 original size:20 final size:20
Alignment explanation
Indices: 40641--40678 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
40631 ATGGCCTCGG
40641 TCGGATGGCCTCGGATGCTC
1 TCGGATGGCCTCGGATGCTC
40661 TCGGATGGCCTCGGATGC
1 TCGGATGGCCTCGGATGC
40679 CCAGCGTGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.11, C:0.29, G:0.37, T:0.24
Consensus pattern (20 bp):
TCGGATGGCCTCGGATGCTC
Found at i:42700 original size:27 final size:25
Alignment explanation
Indices: 42680--42726 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
42670 TTTTAATGTT
42680 ATTT-ATATAA-TTTAAAGTTTTAAG
1 ATTTAATATAATTTTAAA-TTTTAAG
42704 ATTTAATATAATTTTAAATTTTA
1 ATTTAATATAATTTTAAATTTTA
42727 TATTGTACAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 4 0.19
25 11 0.52
26 6 0.29
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (25 bp):
ATTTAATATAATTTTAAATTTTAAG
Found at i:42845 original size:19 final size:19
Alignment explanation
Indices: 42809--42846 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
42799 AAGATAAATG
*
42809 TGATTTTATTATTGACTAC
1 TGATTTTATTAATGACTAC
42828 TGATTTTATTTAAT-ACTAC
1 TGATTTTA-TTAATGACTAC
42847 ACTATTATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.29, C:0.11, G:0.08, T:0.53
Consensus pattern (19 bp):
TGATTTTATTAATGACTAC
Found at i:42954 original size:2 final size:2
Alignment explanation
Indices: 42949--43006 Score: 55
Period size: 2 Copynumber: 29.5 Consensus size: 2
42939 TTCAAAAAAG
* ** *
42949 TA TA TA TA CA TA T- TA TA TA CG TA TA TA TA TG 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
* *
42990 TA TA AA AA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
43007 TTTGAATAGA
Statistics
Matches: 45, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
1 1 0.02
2 44 0.98
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.45
Consensus pattern (2 bp):
TA
Found at i:44036 original size:82 final size:82
Alignment explanation
Indices: 43891--44066 Score: 289
Period size: 82 Copynumber: 2.1 Consensus size: 82
43881 CTGTCATAAT
* * * * * *
43891 CCAACGGCTATAGTTTTAATTTTAAACAGGTAGTATCGATACTACTGTGTTCTAAGTAGCTTCTT
1 CCAACGACTATAGTTTTAATTTTAAACAAGTAGTATCGATACTACTCTGTTATAAGCAACTTCTT
43956 TTGCAAGAATTAAACTC
66 TTGCAAGAATTAAACTC
*
43973 CCAACGATTATAGTTTTAATTTTAAACAAGTAGTATCGATACTACTCTGTTATAAGCAACTTCTT
1 CCAACGACTATAGTTTTAATTTTAAACAAGTAGTATCGATACTACTCTGTTATAAGCAACTTCTT
44038 TTGCAAGAATTAAACTC
66 TTGCAAGAATTAAACTC
44055 CCAACGACTATA
1 CCAACGACTATA
44067 ATTCAACTCT
Statistics
Matches: 86, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
82 86 1.00
ACGTcount: A:0.34, C:0.18, G:0.13, T:0.35
Consensus pattern (82 bp):
CCAACGACTATAGTTTTAATTTTAAACAAGTAGTATCGATACTACTCTGTTATAAGCAACTTCTT
TTGCAAGAATTAAACTC
Found at i:45017 original size:22 final size:21
Alignment explanation
Indices: 44992--45042 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 21
44982 CCAAAATAAT
* *
44992 TAAAAATATTATTTTTATTTAA
1 TAAAAATATTA-ATTTAATTAA
45014 TAAAAATATTAATTTAATTAA
1 TAAAAATATTAATTTAATTAA
45035 -AAAAATAT
1 TAAAAATAT
45043 AATATATAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
20 8 0.30
21 8 0.30
22 11 0.41
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
TAAAAATATTAATTTAATTAA
Found at i:45018 original size:21 final size:21
Alignment explanation
Indices: 44993--45039 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
44983 CAAAATAATT
* * *
44993 AAAAATATTATTTTTATTTAAT
1 AAAAATATTA-ATTTAATTAAA
45015 AAAAATATTAATTTAATTAAA
1 AAAAATATTAATTTAATTAAA
45036 AAAA
1 AAAA
45040 TATAATATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 12 0.55
22 10 0.45
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
AAAAATATTAATTTAATTAAA
Done.