Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009083.1 Hibiscus syriacus cultivar Beakdansim tig00112527_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: 84767
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Found at i:22205 original size:18 final size:19
Alignment explanation
Indices: 22182--22217 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
22172 AAATAACAAC
*
22182 AACAAAA-GAAGGGGAAAA
1 AACAAAATGAAGGAGAAAA
22200 AACAAAATGAAGGAGAAA
1 AACAAAATGAAGGAGAAA
22218 GAAAATAACT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.67, C:0.06, G:0.25, T:0.03
Consensus pattern (19 bp):
AACAAAATGAAGGAGAAAA
Found at i:29970 original size:8 final size:8
Alignment explanation
Indices: 29957--30011 Score: 56
Period size: 8 Copynumber: 6.5 Consensus size: 8
29947 TTATTTAATT
29957 TTAAAAAA
1 TTAAAAAA
*
29965 TTAAAAAT
1 TTAAAAAA
29973 TATAAATAAA
1 T-TAAA-AAA
*
29983 TTAAATAA
1 TTAAAAAA
*
29991 TAAAAAATA
1 TTAAAAA-A
30000 TTAAAAAA
1 TTAAAAAA
30008 TTAA
1 TTAA
30012 GATATTAAAT
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
8 20 0.53
9 15 0.39
10 3 0.08
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (8 bp):
TTAAAAAA
Found at i:29986 original size:26 final size:26
Alignment explanation
Indices: 29957--30020 Score: 69
Period size: 25 Copynumber: 2.5 Consensus size: 26
29947 TTATTTAATT
*
29957 TTAAAAAATTAAAAATTA-TAAATAAA
1 TTAAAAAATTAAAAAATATTAAA-AAA
*
29983 TTAAATAA-TAAAAAATATTAAAAAA
1 TTAAAAAATTAAAAAATATTAAAAAA
* *
30008 TTAAGATATTAAA
1 TTAAAAAATTAAA
30021 TACATCAAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
25 16 0.52
26 15 0.48
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (26 bp):
TTAAAAAATTAAAAAATATTAAAAAA
Found at i:29994 original size:25 final size:25
Alignment explanation
Indices: 29957--30020 Score: 67
Period size: 26 Copynumber: 2.5 Consensus size: 25
29947 TTATTTAATT
* *
29957 TTAAAAAATTAAAAATTA-TAAATAAA
1 TTAAATAA-TAAAAAATATTAAA-AAA
29983 TTAAATAATAAAAAATATTAAAAAA
1 TTAAATAATAAAAAATATTAAAAAA
*
30008 TTAAGATATTAAA
1 TTAA-ATAATAAA
30021 TACATCAAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
25 15 0.45
26 18 0.55
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (25 bp):
TTAAATAATAAAAAATATTAAAAAA
Found at i:30022 original size:42 final size:42
Alignment explanation
Indices: 29957--30037 Score: 103
Period size: 42 Copynumber: 1.9 Consensus size: 42
29947 TTATTTAATT
*
29957 TTAAAAAATTAAAAATTATAAATAAATTAAATAATAAAAAATA
1 TTAAAAAATTAAAAATTATAAATAAATCAAAT-ATAAAAAATA
* *
30000 TTAAAAAATT-AAGA-TATTAAATACATCAAATATAAAAA
1 TTAAAAAATTAAAAATTA-TAAATAAATCAAATATAAAAA
30038 TTCTACAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
41 9 0.26
42 15 0.44
43 10 0.29
ACGTcount: A:0.67, C:0.02, G:0.01, T:0.30
Consensus pattern (42 bp):
TTAAAAAATTAAAAATTATAAATAAATCAAATATAAAAAATA
Found at i:30599 original size:206 final size:210
Alignment explanation
Indices: 30245--30664 Score: 771
Period size: 206 Copynumber: 2.0 Consensus size: 210
30235 TTTCCTAAAC
30245 AATCTTAATAAAAATATTGAAAACATCTTTTTATGTTTTAATATTTTCACTTACTTTTGTTTTCA
1 AATCTTAATAAAAATATTGAAAACATCTTTTTATGTTTTAATATTTTCACTTACTTTTGTTTTCA
30310 TTTTCCAGAAATCATTTTCTAATTTTGTAATCAAACACGTTTTTCTTCAACGTTTCTATTTTCCT
66 TTTTCCAGAAATCATTTTCTAATTTTGTAATCAAACACGTTTTTCTTCAACGTTTCTATTTTCCT
30375 AGAAAATAAAAATG-AA-AATATGTATTTTCTAAACC-AACACACCGTT-AC-TTTCATCTTCAA
131 AGAAAATAAAAATGAAATAATATGTATTTTCTAAACCAAACAC-CCGTTAACTTTTCATCTTCAA
30435 TTATGAATCTCCAACG
195 TTATGAATCTCCAACG
30451 AATCTTAATAAAAATATTGAAAACATCTTTTTATGTTTTAATATTTTCACTTACTTTTGTTTTCA
1 AATCTTAATAAAAATATTGAAAACATCTTTTTATGTTTTAATATTTTCACTTACTTTTGTTTTCA
30516 TTTTCCAGAAATCATTTTCTAATTTTGTAATCAAACACG-TTTTCTTCAACGTTTTCTATTTTCC
66 TTTTCCAGAAATCATTTTCTAATTTTGTAATCAAACACGTTTTTCTTCAACG-TTTCTATTTTCC
30580 TAGAAAATAAAAATGAAAATAATATGTATTTTCTAAACCAAACACCCGTTAACTTTTCATCTTCA
130 TAGAAAATAAAAATG-AAATAATATGTATTTTCTAAACCAAACACCCGTTAACTTTTCATCTTCA
30645 ATTATGAATCTCCAACG
194 ATTATGAATCTCCAACG
30662 AAT
1 AAT
30665 GTTCTTGCTT
Statistics
Matches: 207, Mismatches: 0, Indels: 9
0.96 0.00 0.04
Matches are distributed among these distances:
205 12 0.06
206 131 0.63
208 2 0.01
209 24 0.12
210 7 0.03
211 31 0.15
ACGTcount: A:0.35, C:0.17, G:0.06, T:0.43
Consensus pattern (210 bp):
AATCTTAATAAAAATATTGAAAACATCTTTTTATGTTTTAATATTTTCACTTACTTTTGTTTTCA
TTTTCCAGAAATCATTTTCTAATTTTGTAATCAAACACGTTTTTCTTCAACGTTTCTATTTTCCT
AGAAAATAAAAATGAAATAATATGTATTTTCTAAACCAAACACCCGTTAACTTTTCATCTTCAAT
TATGAATCTCCAACG
Found at i:40308 original size:32 final size:32
Alignment explanation
Indices: 40272--40448 Score: 182
Period size: 32 Copynumber: 5.5 Consensus size: 32
40262 CTCATCTGTA
40272 TATCTGAATGCAATATTAACTCTATTGTGCAT
1 TATCTGAATGCAATATTAACTCTATTGTGCAT
* *
40304 TATCTGAATGTC-ATGTTAACTCTGTTGTGCAT
1 TATCTGAATG-CAATATTAACTCTATTGTGCAT
* * * *
40336 TATCTAAATGCAATACTAATTATATTGTGCAT
1 TATCTGAATGCAATATTAACTCTATTGTGCAT
** *
40368 TATCTGAATGTC-ATGCTAACT-TAACTGTGCAT
1 TATCTGAATG-CAATATTAACTCT-ATTGTGCAT
* *
40400 TATCTCAATGCAATAATT-ACTCTAATGTGCAT
1 TATCTGAATGCAAT-ATTAACTCTATTGTGCAT
*
40432 TATTTGAATGCAATATT
1 TATCTGAATGCAATATT
40449 GACTATGTTG
Statistics
Matches: 120, Mismatches: 18, Indels: 15
0.78 0.12 0.10
Matches are distributed among these distances:
31 6 0.05
32 110 0.92
33 4 0.03
ACGTcount: A:0.31, C:0.15, G:0.13, T:0.41
Consensus pattern (32 bp):
TATCTGAATGCAATATTAACTCTATTGTGCAT
Found at i:40349 original size:64 final size:64
Alignment explanation
Indices: 40272--40441 Score: 218
Period size: 64 Copynumber: 2.7 Consensus size: 64
40262 CTCATCTGTA
* * **
40272 TATCTGAATGCAATATTAACTCTATTGTGCATTATCTGAATGTCATGTTAACTCT-GTTGTGCAT
1 TATCTAAATGCAATATTAACTCTATTGTGCATTATCTGAATGTCATGCTAACT-TAACTGTGCAT
* * *
40336 TATCTAAATGCAATACTAATTATATTGTGCATTATCTGAATGTCATGCTAACTTAACTGTGCAT
1 TATCTAAATGCAATATTAACTCTATTGTGCATTATCTGAATGTCATGCTAACTTAACTGTGCAT
* * *
40400 TATCTCAATGCAATAATT-ACTCTAATGTGCATTATTTGAATG
1 TATCTAAATGCAAT-ATTAACTCTATTGTGCATTATCTGAATG
40442 CAATATTGAC
Statistics
Matches: 91, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
63 1 0.01
64 88 0.97
65 2 0.02
ACGTcount: A:0.31, C:0.15, G:0.14, T:0.41
Consensus pattern (64 bp):
TATCTAAATGCAATATTAACTCTATTGTGCATTATCTGAATGTCATGCTAACTTAACTGTGCAT
Found at i:46661 original size:31 final size:31
Alignment explanation
Indices: 46556--46697 Score: 198
Period size: 31 Copynumber: 4.6 Consensus size: 31
46546 CATTAAACGA
*
46556 CGCACGTTAGCATCTCTCCTTAAGGGGCGCGG
1 CGCACGTTAGCATCTCTCCTTAA-GGGCCCGG
* * *
46588 TGCACATTAGCATCTCTCCTTAAGGG-GC-G
1 CGCACGTTAGCATCTCTCCTTAAGGGCCCGG
46617 CGGCACGTTAGCATCTCTCCTTAAGGGCCCGG
1 C-GCACGTTAGCATCTCTCCTTAAGGGCCCGG
*
46649 CGCATGTTAGCATCTCTCCTTAAGGGCCCGG
1 CGCACGTTAGCATCTCTCCTTAAGGGCCCGG
*
46680 CGCAGGTTAGCATCTCTC
1 CGCACGTTAGCATCTCTC
46698 ACCAATTCTC
Statistics
Matches: 100, Mismatches: 7, Indels: 7
0.88 0.06 0.06
Matches are distributed among these distances:
29 1 0.01
30 26 0.26
31 50 0.50
32 23 0.23
ACGTcount: A:0.17, C:0.32, G:0.27, T:0.25
Consensus pattern (31 bp):
CGCACGTTAGCATCTCTCCTTAAGGGCCCGG
Found at i:46873 original size:4 final size:4
Alignment explanation
Indices: 46864--46896 Score: 50
Period size: 4 Copynumber: 8.5 Consensus size: 4
46854 GGCATCCCCA
*
46864 TTTC TTTC TTTC TTT- TTAC TTTC TTTC TTTC TT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TT
46897 CATCTCTCAC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
3 2 0.08
4 24 0.92
ACGTcount: A:0.03, C:0.21, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTC
Found at i:58374 original size:2 final size:2
Alignment explanation
Indices: 58367--58401 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
58357 TATGTAATTG
58367 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
58402 AAACAAAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:58466 original size:18 final size:18
Alignment explanation
Indices: 58431--58474 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
58421 TTATCAATTC
*
58431 ATAAATAAATGTATAAAT
1 ATAAATAAATATATAAAT
58449 ATAAA-AAATATATCAAAT
1 ATAAATAAATATAT-AAAT
58467 ATATAATA
1 ATA-AATA
58475 TCATAAAGCC
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 7 0.32
18 12 0.55
19 2 0.09
20 1 0.05
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (18 bp):
ATAAATAAATATATAAAT
Found at i:63782 original size:31 final size:32
Alignment explanation
Indices: 63725--63804 Score: 78
Period size: 31 Copynumber: 2.6 Consensus size: 32
63715 TTTTGTAGTC
*
63725 AAAATAAATATTTAAA-T-TTATCTTTTTGATA
1 AAAATAAATATATAAAGTATTATCTTTTT-ATA
* *
63756 AAAATAAATATATAAAGTATT-T-TTTTTTTC
1 AAAATAAATATATAAAGTATTATCTTTTTATA
**
63786 AAAATAAATACCTAAAGTA
1 AAAATAAATATATAAAGTA
63805 CTTAACTATT
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
30 18 0.43
31 20 0.48
32 2 0.05
33 2 0.05
ACGTcount: A:0.49, C:0.05, G:0.04, T:0.42
Consensus pattern (32 bp):
AAAATAAATATATAAAGTATTATCTTTTTATA
Found at i:63790 original size:30 final size:30
Alignment explanation
Indices: 63723--63804 Score: 83
Period size: 30 Copynumber: 2.7 Consensus size: 30
63713 TATTTTGTAG
* *
63723 TCAAAATAAATATTTAAATTTATCTTTTTGA
1 TCAAAATAAATATATAAA-GTATCTTTTTGA
* * **
63754 TAAAAATAAATATATAAAGTATTTTTTTTT
1 TCAAAATAAATATATAAAGTATCTTTTTGA
**
63784 TCAAAATAAATACCTAAAGTA
1 TCAAAATAAATATATAAAGTA
63805 CTTAACTATT
Statistics
Matches: 42, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
30 26 0.62
31 16 0.38
ACGTcount: A:0.48, C:0.06, G:0.04, T:0.43
Consensus pattern (30 bp):
TCAAAATAAATATATAAAGTATCTTTTTGA
Found at i:66682 original size:3 final size:3
Alignment explanation
Indices: 66674--66723 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
66664 CAAGCACTTC
66674 CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT
1 CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT
66722 CC
1 CC
66724 AGTGCAGGTT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.00, C:0.68, G:0.00, T:0.32
Consensus pattern (3 bp):
CCT
Found at i:68294 original size:21 final size:22
Alignment explanation
Indices: 68263--68303 Score: 75
Period size: 21 Copynumber: 1.9 Consensus size: 22
68253 CTTAGACTTA
68263 AGGGGATGAACTAAAATTCTTG
1 AGGGGATGAACTAAAATTCTTG
68285 AGGGG-TGAACTAAAATTCT
1 AGGGGATGAACTAAAATTCT
68304 AGTGGTGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.37, C:0.10, G:0.27, T:0.27
Consensus pattern (22 bp):
AGGGGATGAACTAAAATTCTTG
Found at i:73574 original size:33 final size:33
Alignment explanation
Indices: 73492--73559 Score: 100
Period size: 33 Copynumber: 2.1 Consensus size: 33
73482 AGAATCAGCG
*
73492 TTGAAGCAATTAACATCGAATATTGAGGCATCT
1 TTGAAGAAATTAACATCGAATATTGAGGCATCT
* * *
73525 TTGAAGAAATCAACATCGAATGTTGGGGCATCT
1 TTGAAGAAATTAACATCGAATATTGAGGCATCT
73558 TT
1 TT
73560 AGGGATTTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.34, C:0.15, G:0.21, T:0.31
Consensus pattern (33 bp):
TTGAAGAAATTAACATCGAATATTGAGGCATCT
Found at i:73770 original size:37 final size:37
Alignment explanation
Indices: 73714--73793 Score: 99
Period size: 37 Copynumber: 2.2 Consensus size: 37
73704 TCTTTAGTTT
* *
73714 GTTTCCTTTGAAATAAAATTGTGTCTCATTTGAGACA
1 GTTTCCTTCGAAATAAAATTGTGTCTCACTTGAGACA
* *
73751 GTTTCCTTCGAAA-ACAAATTTTGTCTCGCTTGAGACA
1 GTTTCCTTCGAAATA-AAATTGTGTCTCACTTGAGACA
*
73788 TTTTCC
1 GTTTCC
73794 CTTTGAGATA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
36 1 0.03
37 36 0.97
ACGTcount: A:0.26, C:0.19, G:0.15, T:0.40
Consensus pattern (37 bp):
GTTTCCTTCGAAATAAAATTGTGTCTCACTTGAGACA
Found at i:73884 original size:35 final size:35
Alignment explanation
Indices: 73828--73963 Score: 125
Period size: 36 Copynumber: 3.8 Consensus size: 35
73818 GTTTCACATT
* *
73828 AAACAAAGTTGATCTCACTTGAGATCGTTT-TCTCA
1 AAACAAATTTG-TCTCACTTGAGATCATTTCTCTCA
* *
73863 AAACAAACTTTGTCTCGCTTGAGA-CAATTTCTCTAA
1 AAACAAA-TTTGTCTCACTTGAGATC-ATTTCTCTCA
* * *
73899 AAACAAATTTTGTCTCTCTTAAGATAATTTCTCTCA
1 AAACAAA-TTTGTCTCACTTGAGATCATTTCTCTCA
* *
73935 AAGCAAATTTCATCTCACTTGAGA-CATTT
1 AAACAAATTT-GTCTCACTTGAGATCATTT
73964 TTTTCTCTGA
Statistics
Matches: 82, Mismatches: 14, Indels: 10
0.77 0.13 0.09
Matches are distributed among these distances:
34 1 0.01
35 28 0.34
36 53 0.65
ACGTcount: A:0.33, C:0.21, G:0.10, T:0.36
Consensus pattern (35 bp):
AAACAAATTTGTCTCACTTGAGATCATTTCTCTCA
Found at i:74258 original size:26 final size:26
Alignment explanation
Indices: 74212--74278 Score: 80
Period size: 26 Copynumber: 2.5 Consensus size: 26
74202 GAGACAATTT
74212 CTTTTGAAATAAATCTTTGAGTATGTTC
1 CTTTTG-AA-AAATCTTTGAGTATGTTC
* *
74240 CTTTTGAAAAATCTTTGAGTTTGTTT
1 CTTTTGAAAAATCTTTGAGTATGTTC
* *
74266 CTCTTAAAAAATC
1 CTTTTGAAAAATC
74279 ATCTTTGAGG
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
26 27 0.77
27 2 0.06
28 6 0.17
ACGTcount: A:0.30, C:0.12, G:0.12, T:0.46
Consensus pattern (26 bp):
CTTTTGAAAAATCTTTGAGTATGTTC
Found at i:76220 original size:28 final size:30
Alignment explanation
Indices: 76161--76230 Score: 83
Period size: 29 Copynumber: 2.4 Consensus size: 30
76151 GAGTTTCTGT
* *
76161 TTTTGCTATTTTAATCCTTTAAATGTTTTG
1 TTTTGCTATTTTAAGCCTTTAAATGTTATG
76191 TTTT-CTATTTT-AGCCTTTTAAAT-TTATG
1 TTTTGCTATTTTAAGCC-TTTAAATGTTATG
*
76219 TTTTGTTATTTT
1 TTTTGCTATTTT
76231 GGGTCCTTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
28 11 0.31
29 20 0.57
30 4 0.11
ACGTcount: A:0.19, C:0.09, G:0.09, T:0.64
Consensus pattern (30 bp):
TTTTGCTATTTTAAGCCTTTAAATGTTATG
Found at i:79429 original size:25 final size:26
Alignment explanation
Indices: 79376--79437 Score: 85
Period size: 25 Copynumber: 2.5 Consensus size: 26
79366 TTTCTTTACA
* *
79376 ATTTACTTTTC-TTATTTTTAATTTT
1 ATTTACTTTACTTTAATTTTAATTTT
79401 -TTTACTTTACTTTAATTTT-ATTTT
1 ATTTACTTTACTTTAATTTTAATTTT
79425 ATTTACTTTACTT
1 ATTTACTTTACTT
79438 GATTATTTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
24 14 0.42
25 19 0.58
ACGTcount: A:0.21, C:0.10, G:0.00, T:0.69
Consensus pattern (26 bp):
ATTTACTTTACTTTAATTTTAATTTT
Found at i:79431 original size:20 final size:19
Alignment explanation
Indices: 79392--79434 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 19
79382 TTTTCTTATT
79392 TTTAATTTTTTTACTTTAC
1 TTTAATTTTTTTACTTTAC
79411 TTTAATTTTATTTTA-TTTAC
1 TTTAA-TTT-TTTTACTTTAC
79431 TTTA
1 TTTA
79435 CTTGATTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 5 0.23
20 12 0.55
21 5 0.23
ACGTcount: A:0.23, C:0.07, G:0.00, T:0.70
Consensus pattern (19 bp):
TTTAATTTTTTTACTTTAC
Done.