Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004835.1 Hibiscus syriacus cultivar Beakdansim tig00010895_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: 57685
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:14783 original size:39 final size:37
Alignment explanation
Indices: 14706--14813 Score: 119
Period size: 39 Copynumber: 2.8 Consensus size: 37
14696 CTTGGTTATC
* *
14706 AAATTATTTATCCTAGCATTCTAAATT-TCTAATTTCTT
1 AAATTATTTA-CCTAACATTCTAAATTAT-TAATGTCTT
*
14744 AAATTATTTCACCATAACATTTTAAATTATTAATGTCTT
1 AAATTATTT-ACC-TAACATTCTAAATTATTAATGTCTT
*
14783 AAATTATTTTACCCTAACAATCTAAATTATT
1 AAATTA-TTTA-CCTAACATTCTAAATTATT
14814 TCTCAAATTA
Statistics
Matches: 60, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
38 11 0.18
39 43 0.72
40 6 0.10
ACGTcount: A:0.37, C:0.15, G:0.02, T:0.46
Consensus pattern (37 bp):
AAATTATTTACCTAACATTCTAAATTATTAATGTCTT
Found at i:14898 original size:34 final size:34
Alignment explanation
Indices: 14855--14948 Score: 100
Period size: 34 Copynumber: 2.7 Consensus size: 34
14845 TTAAATTTAA
*
14855 TTATGTTTTTAAATTTTATCTTTTAATTATGTAT
1 TTATATTTTTAAATTTTATCTTTTAATTATGTAT
* ** *
14889 TTATCTTTTTAAATTTTATGC-GCTGATTATGTAT
1 TTATATTTTTAAATTTTAT-CTTTTAATTATGTAT
* *
14923 TATATATCTTTAAATTTTATATTTTA
1 T-TATATTTTTAAATTTTATCTTTTA
14949 TATGTAAGAT
Statistics
Matches: 47, Mismatches: 10, Indels: 5
0.76 0.16 0.08
Matches are distributed among these distances:
34 29 0.62
35 18 0.38
ACGTcount: A:0.28, C:0.05, G:0.06, T:0.61
Consensus pattern (34 bp):
TTATATTTTTAAATTTTATCTTTTAATTATGTAT
Found at i:16114 original size:16 final size:15
Alignment explanation
Indices: 16093--16122 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
16083 GATTTTTAGT
16093 ATAAATAGAGGTGTTA
1 ATAAATAGA-GTGTTA
16109 ATAAATAGAGTGTT
1 ATAAATAGAGTGTT
16123 CGATGAATTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.43, C:0.00, G:0.23, T:0.33
Consensus pattern (15 bp):
ATAAATAGAGTGTTA
Found at i:27179 original size:42 final size:42
Alignment explanation
Indices: 27133--27249 Score: 198
Period size: 42 Copynumber: 2.8 Consensus size: 42
27123 CTCCGAATTC
*
27133 CCGTGTTTGTTTCACGTAATTCGTTTTTCGGAAAATGTTTTT
1 CCGTGTTTGTTTCACGTAATTCGTTTTTCGGAAAACGTTTTT
* *
27175 CCGTGTTTATTTCACGTAATTCGTTTTTCGAAAAACGTTTTT
1 CCGTGTTTGTTTCACGTAATTCGTTTTTCGGAAAACGTTTTT
*
27217 CCGTGTTTGTTTCACGTAATTCGTTTTCCGGAA
1 CCGTGTTTGTTTCACGTAATTCGTTTTTCGGAA
27250 TGTAATTCAT
Statistics
Matches: 69, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 69 1.00
ACGTcount: A:0.18, C:0.17, G:0.18, T:0.47
Consensus pattern (42 bp):
CCGTGTTTGTTTCACGTAATTCGTTTTTCGGAAAACGTTTTT
Found at i:27481 original size:23 final size:23
Alignment explanation
Indices: 27438--27528 Score: 60
Period size: 21 Copynumber: 3.8 Consensus size: 23
27428 TAATTATTAA
* *
27438 AATATTTAAAAT-ATAT-TTATT
1 AATATTTATAATAATATAATATT
27459 AATATTTATAATAATATAATATT
1 AATATTTATAATAATATAATATT
* * * * *
27482 ATTTTTTAATATTATATAAAATAATC
1 AATATTT-ATAATA-ATATAAT-ATT
27508 AATTATATTATAATAATATAA
1 AA-TAT-TTATAATAATATAA
27529 GATATTATAT
Statistics
Matches: 52, Mismatches: 11, Indels: 9
0.72 0.15 0.12
Matches are distributed among these distances:
21 11 0.21
22 4 0.08
23 9 0.17
24 5 0.10
25 6 0.12
26 8 0.15
27 7 0.13
28 2 0.04
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (23 bp):
AATATTTATAATAATATAATATT
Found at i:27483 original size:26 final size:24
Alignment explanation
Indices: 27421--27484 Score: 62
Period size: 23 Copynumber: 2.6 Consensus size: 24
27411 CATTTTCATC
27421 AAAATAT-TAATTATTAAAATATTT
1 AAAATATAT-ATTATTAAAATATTT
*
27445 AAAATATAT-TTATTAATAT-TTAT
1 AAAATATATATTATTAAAATATT-T
27468 AATAATATAATATTATT
1 AA-AATAT-ATATTATT
27485 TTTTAATATT
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
22 2 0.06
23 12 0.35
24 12 0.35
25 3 0.09
26 5 0.15
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (24 bp):
AAAATATATATTATTAAAATATTT
Found at i:27485 original size:30 final size:30
Alignment explanation
Indices: 27447--27614 Score: 86
Period size: 30 Copynumber: 6.0 Consensus size: 30
27437 AAATATTTAA
27447 AATA-TATTTATTAATATTTATAATAATAT
1 AATATTATTTATTAATATTTATAATAATAT
*
27476 AATATTATTTTTTAATA-TTAT-AT-A-A-
1 AATATTATTTATTAATATTTATAATAATAT
**
27501 AATA--ATCAATT-ATA-TTATAATAATAT
1 AATATTATTTATTAATATTTATAATAATAT
*
27527 AAGATATTATATT-TTTAT-TTTAATAAT-ATAT
1 -A-ATATTAT-TTATTAATATTT-ATAATAATAT
*
27558 AATAATT-TTT-TTATATATTTAATAATGA-AT
1 AAT-ATTATTTATTA-ATATTT-ATAATAATAT
*
27588 AATATTATTTA-T-ATATTT-CAATAATAT
1 AATATTATTTATTAATATTTATAATAATAT
27615 TTTAGTAAAG
Statistics
Matches: 110, Mismatches: 9, Indels: 42
0.68 0.06 0.26
Matches are distributed among these distances:
22 7 0.06
23 6 0.05
24 1 0.01
25 5 0.05
26 5 0.05
27 4 0.04
28 15 0.14
29 16 0.15
30 37 0.34
31 9 0.08
32 5 0.05
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.52
Consensus pattern (30 bp):
AATATTATTTATTAATATTTATAATAATAT
Found at i:27505 original size:33 final size:34
Alignment explanation
Indices: 27430--27506 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 34
27420 CAAAATATTA
*
27430 ATTAT-TAAAAT-ATTTAAAATATATTTATTAAT
1 ATTATATAAAATAATATAAAATATATTTATTAAT
* *
27462 ATT-TAT--AATAATATAATAT-TATTTTTTAAT
1 ATTATATAAAATAATATAAAATATATTTATTAAT
27492 ATTATATAAAATAAT
1 ATTATATAAAATAAT
27507 CAATTATATT
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
30 16 0.43
31 11 0.30
32 4 0.11
33 6 0.16
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (34 bp):
ATTATATAAAATAATATAAAATATATTTATTAAT
Found at i:27858 original size:20 final size:20
Alignment explanation
Indices: 27780--27849 Score: 122
Period size: 20 Copynumber: 3.5 Consensus size: 20
27770 TTTCCAGATG
*
27780 TTTTCCATAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
27800 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
*
27820 TTTTACAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
27840 TTTTCCAGAA
1 TTTTCCAGAA
27850 TTCAAATTCC
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.36, C:0.14, G:0.09, T:0.41
Consensus pattern (20 bp):
TTTTCCAGAAATGTAATTCA
Found at i:27868 original size:15 final size:15
Alignment explanation
Indices: 27832--27913 Score: 121
Period size: 15 Copynumber: 5.5 Consensus size: 15
27822 TTACAGAAAT
**
27832 GTAATTCATTTTCCA
1 GTAATTCAAATTCCA
27847 G-AATTCAAATTCCA
1 GTAATTCAAATTCCA
**
27861 GTAATTCATTTTCCA
1 GTAATTCAAATTCCA
27876 GTAATTCAAATTCCA
1 GTAATTCAAATTCCA
27891 GTAATTCAAATTCCA
1 GTAATTCAAATTCCA
27906 GTAATTCA
1 GTAATTCA
27914 TTTTCTGAAA
Statistics
Matches: 60, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
14 12 0.20
15 48 0.80
ACGTcount: A:0.35, C:0.20, G:0.07, T:0.38
Consensus pattern (15 bp):
GTAATTCAAATTCCA
Found at i:27884 original size:30 final size:30
Alignment explanation
Indices: 27832--27913 Score: 139
Period size: 30 Copynumber: 2.8 Consensus size: 30
27822 TTACAGAAAT
27832 GTAATTCATTTTCCAG-AATTCAAATTCCA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
27861 GTAATTCATTTTCCAGTAATTCAAATTCCA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
**
27891 GTAATTCAAATTCCAGTAATTCA
1 GTAATTCATTTTCCAGTAATTCA
27914 TTTTCTGAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 16 0.32
30 34 0.68
ACGTcount: A:0.35, C:0.20, G:0.07, T:0.38
Consensus pattern (30 bp):
GTAATTCATTTTCCAGTAATTCAAATTCCA
Found at i:27906 original size:45 final size:44
Alignment explanation
Indices: 27832--27918 Score: 147
Period size: 45 Copynumber: 2.0 Consensus size: 44
27822 TTACAGAAAT
**
27832 GTAATTCATTTTCCAGAATTCAAATTCCAGTAATTCATTTTCCA
1 GTAATTCAAATTCCAGAATTCAAATTCCAGTAATTCATTTTCCA
27876 GTAATTCAAATTCCAGTAATTCAAATTCCAGTAATTCATTTTC
1 GTAATTCAAATTCCAG-AATTCAAATTCCAGTAATTCATTTTC
27919 TGAAAAACCA
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
44 14 0.35
45 26 0.65
ACGTcount: A:0.33, C:0.20, G:0.07, T:0.40
Consensus pattern (44 bp):
GTAATTCAAATTCCAGAATTCAAATTCCAGTAATTCATTTTCCA
Found at i:47607 original size:7 final size:8
Alignment explanation
Indices: 47578--47606 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
47568 TTTTAAATTC
47578 ATTTTTAA
1 ATTTTTAA
47586 ATTTTTAA
1 ATTTTTAA
47594 ATTTTTAA
1 ATTTTTAA
47602 ATTTT
1 ATTTT
47607 ATTTCTAAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (8 bp):
ATTTTTAA
Found at i:47889 original size:60 final size:61
Alignment explanation
Indices: 47718--47894 Score: 163
Period size: 63 Copynumber: 2.9 Consensus size: 61
47708 TCAAATATTA
* * *
47718 TAATTTCAT--TCCCAAACTATGACATTCATTCTAAATTGGTCTTCAAAA-TTTTTAACATTC
1 TAATTTCATCCTCTCAAACTATGACCTTCATTCTAAATTGGTC--CAAAACTTTTAAACATTC
* * *
47778 TAATTTTATCCTCCTCAAACTATGA-CTCTCATTCTGAATTAATGTCC-AAACTTTTAAACATT-
1 TAATTTCATCCT-CTCAAACTATGACCT-TCATTCTAAATT--GGTCCAAAACTTTTAAACATTC
*
47840 TCAATTTCAT-CT-TCAAACTATAACCTTCATTCTAAATTGGTCCATAAACTTTTAA
1 T-AATTTCATCCTCTCAAACTATGACCTTCATTCTAAATTGGTCCA-AAACTTTTAA
47895 TATCTTAATT
Statistics
Matches: 96, Mismatches: 10, Indels: 22
0.75 0.08 0.17
Matches are distributed among these distances:
58 4 0.04
60 39 0.41
61 2 0.02
62 8 0.08
63 40 0.42
65 3 0.03
ACGTcount: A:0.33, C:0.21, G:0.05, T:0.41
Consensus pattern (61 bp):
TAATTTCATCCTCTCAAACTATGACCTTCATTCTAAATTGGTCCAAAACTTTTAAACATTC
Found at i:49020 original size:20 final size:20
Alignment explanation
Indices: 48995--49032 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
48985 TTTGGTTCAC
48995 GGAATGTAAAATTACTAGTG
1 GGAATGTAAAATTACTAGTG
*
49015 GGAATGTAAGATTACTAG
1 GGAATGTAAAATTACTAG
49033 GGAATAAGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.39, C:0.05, G:0.26, T:0.29
Consensus pattern (20 bp):
GGAATGTAAAATTACTAGTG
Found at i:49268 original size:39 final size:36
Alignment explanation
Indices: 49186--49268 Score: 85
Period size: 39 Copynumber: 2.2 Consensus size: 36
49176 TAACAAGTTG
* * *
49186 AAAAATATTTATATATTTTCTTTAAAAATTTAAATT
1 AAAAAAATTTATATATTTTCTTTAAAAATTGAAAAT
* * *
49222 CATAAAATTTATATAATTTTTTTTTACAAAATTGAAAAT
1 AAAAAAATTTATAT-A-TTTTCTTTA-AAAATTGAAAAT
49261 AAAAAAAT
1 AAAAAAAT
49269 ATTTAATGAA
Statistics
Matches: 36, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
36 11 0.31
37 1 0.03
38 8 0.22
39 16 0.44
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.45
Consensus pattern (36 bp):
AAAAAAATTTATATATTTTCTTTAAAAATTGAAAAT
Found at i:51785 original size:19 final size:20
Alignment explanation
Indices: 51763--51816 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
51753 AAATCGCAAC
51763 GCGATTTT-AGTTTCGCGTT
1 GCGATTTTAAGTTTCGCGTT
* *
51782 GCGATTTTCATTTTCGCGTT
1 GCGATTTTAAGTTTCGCGTT
51802 GCGATTTTAAGTTTC
1 GCGATTTTAAGTTTC
51817 AGAAACTATT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
19 8 0.26
20 23 0.74
ACGTcount: A:0.13, C:0.17, G:0.22, T:0.48
Consensus pattern (20 bp):
GCGATTTTAAGTTTCGCGTT
Found at i:53550 original size:21 final size:23
Alignment explanation
Indices: 53526--53642 Score: 83
Period size: 21 Copynumber: 5.5 Consensus size: 23
53516 TGGTGCATGG
53526 CGTGATGAGGTA-CGGT-CTTTA
1 CGTGATGAGGTATCGGTACTTTA
* **
53547 CGTGGTGAGGTAGAGGT--TTTA
1 CGTGATGAGGTATCGGTACTTTA
* ** *
53568 CGCGATGA-CAAT-GGTGCTTTA
1 CGTGATGAGGTATCGGTACTTTA
*
53589 CGTGGTGAGGTATC--TACTTTA
1 CGTGATGAGGTATCGGTACTTTA
53610 CGTGATGAGGTATC--TACTTTA
1 CGTGATGAGGTATCGGTACTTTA
*
53631 CGTGATAAGGTA
1 CGTGATGAGGTA
53643 GCCGCTCTAC
Statistics
Matches: 77, Mismatches: 14, Indels: 10
0.76 0.14 0.10
Matches are distributed among these distances:
19 3 0.04
20 1 0.01
21 68 0.88
22 5 0.06
ACGTcount: A:0.22, C:0.13, G:0.32, T:0.33
Consensus pattern (23 bp):
CGTGATGAGGTATCGGTACTTTA
Found at i:53779 original size:12 final size:12
Alignment explanation
Indices: 53753--53794 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
53743 TTTTTCGGCA
53753 TTATTTATTTG-T
1 TTATTTA-TTGAT
53765 TTATTTATTGAT
1 TTATTTATTGAT
* *
53777 TTATGTATTAAT
1 TTATTTATTGAT
53789 TTATTT
1 TTATTT
53795 TTAGCGGCCC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
11 3 0.12
12 23 0.88
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.69
Consensus pattern (12 bp):
TTATTTATTGAT
Found at i:53984 original size:42 final size:42
Alignment explanation
Indices: 53937--54037 Score: 123
Period size: 42 Copynumber: 2.4 Consensus size: 42
53927 TCGATTCACC
*
53937 TGTCATCGTTCAATAGGACTCTCCT-ATCGTTTAAGAGGCCCT
1 TGTCATCGTTCAAGAGGACT-TCCTCATCGTTTAAGAGGCCCT
* ** * *
53979 TGTCATCGTTCAAGAGGCCTTTGTCATTGTTTAAGAGGCCTT
1 TGTCATCGTTCAAGAGGACTTCCTCATCGTTTAAGAGGCCCT
*
54021 TGTCATCATTCAAGAGG
1 TGTCATCGTTCAAGAGG
54038 TCCCTCCCAC
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
41 2 0.04
42 49 0.96
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.35
Consensus pattern (42 bp):
TGTCATCGTTCAAGAGGACTTCCTCATCGTTTAAGAGGCCCT
Found at i:53986 original size:21 final size:21
Alignment explanation
Indices: 53962--54042 Score: 99
Period size: 21 Copynumber: 3.8 Consensus size: 21
53952 GGACTCTCCT
*
53962 ATCGTTTAAGAGGCCCTTGTC
1 ATCGTTCAAGAGGCCCTTGTC
*
53983 ATCGTTCAAGAGGCCTTTGTC
1 ATCGTTCAAGAGGCCCTTGTC
* * *
54004 ATTGTTTAAGAGGCCTTTGTC
1 ATCGTTCAAGAGGCCCTTGTC
*
54025 ATCATTCAAGAGGTCCCT
1 ATCGTTCAAGAGG-CCCT
54043 CCCACCGTTC
Statistics
Matches: 51, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
21 48 0.94
22 3 0.06
ACGTcount: A:0.21, C:0.22, G:0.22, T:0.35
Consensus pattern (21 bp):
ATCGTTCAAGAGGCCCTTGTC
Found at i:55960 original size:18 final size:18
Alignment explanation
Indices: 55937--55972 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
55927 AAGTCGGTTG
*
55937 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
55955 TGATTGCGATTTTGATTT
1 TGATTGCGATTTTGATTT
55973 CCTTTTGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.03, G:0.25, T:0.56
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:56885 original size:30 final size:30
Alignment explanation
Indices: 56849--56912 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
56839 GAAGGACCTG
*
56849 TCCAGAGGTTACAAAGAACCCCGGTAACTA
1 TCCAGAGGTCACAAAGAACCCCGGTAACTA
* * *
56879 TCCAGAGGTCATAAAGATCCTCGGTAACTA
1 TCCAGAGGTCACAAAGAACCCCGGTAACTA
56909 TCCA
1 TCCA
56913 TATGTTCCTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.34, C:0.27, G:0.19, T:0.20
Consensus pattern (30 bp):
TCCAGAGGTCACAAAGAACCCCGGTAACTA
Done.