Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004718.1 Hibiscus syriacus cultivar Beakdansim tig00010638_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: 46970
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Found at i:2802 original size:24 final size:23
Alignment explanation
Indices: 2770--2832 Score: 99
Period size: 24 Copynumber: 2.7 Consensus size: 23
2760 TGCCACATAG
2770 AAATGCACCAAAGTGTCGCGTATA
1 AAATGCACCAAAGTGTCGCGTA-A
2794 AAATGCACCAAAGTGTCGCGTAA
1 AAATGCACCAAAGTGTCGCGTAA
*
2817 AATATGAACCAAAGTG
1 AA-ATGCACCAAAGTG
2833 CCACATAAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
23 3 0.08
24 34 0.92
ACGTcount: A:0.41, C:0.19, G:0.21, T:0.19
Consensus pattern (23 bp):
AAATGCACCAAAGTGTCGCGTAA
Found at i:2841 original size:24 final size:23
Alignment explanation
Indices: 2760--2845 Score: 82
Period size: 24 Copynumber: 3.7 Consensus size: 23
2750 TAGTCGAAAC
*
2760 TGCCACATAGAAATGCACCAAAG
1 TGCCACATAAAAATGCACCAAAG
* * *
2783 TGTCGCGTATAAAATGCACCAAAG
1 TGCCACATA-AAAATGCACCAAAG
* * * *
2807 TGTCGCGTAAAATATGAACCAAAG
1 TGCCACATAAAA-ATGCACCAAAG
2831 TGCCACATAAAAATG
1 TGCCACATAAAAATG
2846 TCTGAAGGAC
Statistics
Matches: 53, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
23 12 0.23
24 41 0.77
ACGTcount: A:0.42, C:0.21, G:0.19, T:0.19
Consensus pattern (23 bp):
TGCCACATAAAAATGCACCAAAG
Found at i:2866 original size:22 final size:22
Alignment explanation
Indices: 2841--2925 Score: 64
Period size: 23 Copynumber: 3.7 Consensus size: 22
2831 TGCCACATAA
*
2841 AAATGTCTGAAGGACCACGTAG
1 AAATGTCCGAAGGACCACGTAG
* *
2863 AAATATCCCGAATGACCACGTAG
1 AAATGT-CCGAAGGACCACGTAG
* *
2886 AATATGTCCCAAAGGACC-CATAG
1 AA-ATGT-CCGAAGGACCACGTAG
* *
2909 AATTATCCTGAAGGACC
1 AAATGTCC-GAAGGACC
2926 GCATAGAACC
Statistics
Matches: 50, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
21 2 0.04
22 14 0.28
23 22 0.44
24 12 0.24
ACGTcount: A:0.38, C:0.24, G:0.20, T:0.19
Consensus pattern (22 bp):
AAATGTCCGAAGGACCACGTAG
Found at i:2903 original size:24 final size:24
Alignment explanation
Indices: 2850--2925 Score: 77
Period size: 23 Copynumber: 3.3 Consensus size: 24
2840 AAAATGTCTG
*
2850 AAGGACCACGTAGAA-ATATCCCG
1 AAGGACCACGTAGAATATATCCCA
* *
2873 AATGACCACGTAGAATATGTCCCA
1 AAGGACCACGTAGAATATATCCCA
* **
2897 AAGGACC-CATAGAAT-TATCCTG
1 AAGGACCACGTAGAATATATCCCA
2919 AAGGACC
1 AAGGACC
2926 GCATAGAACC
Statistics
Matches: 44, Mismatches: 8, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
22 11 0.25
23 21 0.48
24 12 0.27
ACGTcount: A:0.38, C:0.25, G:0.20, T:0.17
Consensus pattern (24 bp):
AAGGACCACGTAGAATATATCCCA
Found at i:3082 original size:15 final size:15
Alignment explanation
Indices: 3064--3146 Score: 58
Period size: 15 Copynumber: 5.4 Consensus size: 15
3054 ATAGGGTATC
3064 TTCACGTAGAACATT
1 TTCACGTAGAACATT
* *
3079 TTCACTTAGCACATT
1 TTCACGTAGAACATT
* ** * *
3094 ATCATATATAATCCTT
1 TTCACGTAGAA-CATT
* *
3110 TTAAGGTAGAACATTT
1 TTCACGTAGAACA-TT
*
3126 TTCACGTAGAACAGT
1 TTCACGTAGAACATT
3141 TTCACG
1 TTCACG
3147 AAAATTTATC
Statistics
Matches: 49, Mismatches: 17, Indels: 4
0.70 0.24 0.06
Matches are distributed among these distances:
15 27 0.55
16 22 0.45
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.36
Consensus pattern (15 bp):
TTCACGTAGAACATT
Found at i:6860 original size:21 final size:21
Alignment explanation
Indices: 6821--6861 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
6811 CCATGGACAA
* *
6821 TGCTACAGTGCATCGATGCAT
1 TGCTACAGTGCACCAATGCAT
6842 TGCTACAGTGCACCAATGCA
1 TGCTACAGTGCACCAATGCA
6862 CTAAAATTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.24
Consensus pattern (21 bp):
TGCTACAGTGCACCAATGCAT
Found at i:9241 original size:16 final size:17
Alignment explanation
Indices: 9208--9241 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
9198 TATGAATGGT
9208 TTTATAAACTTGTATTA
1 TTTATAAACTTGTATTA
*
9225 TTTATAAA-TTGTTTTA
1 TTTATAAACTTGTATTA
9241 T
1 T
9242 GATTTTACGC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.32, C:0.03, G:0.06, T:0.59
Consensus pattern (17 bp):
TTTATAAACTTGTATTA
Found at i:9475 original size:2 final size:2
Alignment explanation
Indices: 9470--9516 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
9460 TCTATTATTA
9470 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
9511 AT AT AT
1 AT AT AT
9517 CACTCTTAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 43 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:10487 original size:14 final size:14
Alignment explanation
Indices: 10468--10494 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
10458 ATCAAGTTAT
10468 GCAAATATTAGGGG
1 GCAAATATTAGGGG
10482 GCAAATATTAGGG
1 GCAAATATTAGGG
10495 TTTAAGAACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.07, G:0.33, T:0.22
Consensus pattern (14 bp):
GCAAATATTAGGGG
Found at i:17774 original size:22 final size:23
Alignment explanation
Indices: 17728--17801 Score: 71
Period size: 21 Copynumber: 3.1 Consensus size: 23
17718 ATACAATAAA
**
17728 TAATATTATTTATCATAAAAT-T
1 TAATATTATTTATTTTAAAATAT
17750 TAATATTA-TTATTTTAAAATAT
1 TAATATTATTTATTTTAAAATAT
17772 TAAAATAATTTATTTATTATTAAAATAT
1 T--AAT-A-TTATTTATT-TTAAAATAT
17800 TA
1 TA
17802 TTTTTATAAT
Statistics
Matches: 43, Mismatches: 2, Indels: 10
0.78 0.04 0.18
Matches are distributed among these distances:
21 10 0.23
22 10 0.23
24 3 0.07
25 1 0.02
26 4 0.09
27 5 0.12
28 10 0.23
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.51
Consensus pattern (23 bp):
TAATATTATTTATTTTAAAATAT
Found at i:17931 original size:23 final size:23
Alignment explanation
Indices: 17902--17946 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
17892 AGTGTTATAT
17902 TATATTTTAAAAATATTAATTAG
1 TATATTTTAAAAATATTAATTAG
* *
17925 TATATTTTAAATATATTTATTA
1 TATATTTTAAAAATATTAATTA
17947 AAATATTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (23 bp):
TATATTTTAAAAATATTAATTAG
Found at i:17952 original size:23 final size:23
Alignment explanation
Indices: 17903--17953 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
17893 GTGTTATATT
**
17903 ATATTTTAAAAATATTAATTAGT
1 ATATTTTAAAAATATTAATTAAA
* *
17926 ATATTTTAAATATATTTATTAAA
1 ATATTTTAAAAATATTAATTAAA
17949 ATATT
1 ATATT
17954 ATATTAATAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (23 bp):
ATATTTTAAAAATATTAATTAAA
Found at i:17958 original size:17 final size:19
Alignment explanation
Indices: 17936--17972 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
17926 ATATTTTAAA
17936 TATATT-TATTAAA-ATAT
1 TATATTATATTAAATATAT
17953 TATATTAATATTAAATATAT
1 TATATT-ATATTAAATATAT
17973 AAATAATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
17 6 0.35
19 7 0.41
20 4 0.24
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
TATATTATATTAAATATAT
Found at i:17964 original size:34 final size:31
Alignment explanation
Indices: 17902--17972 Score: 81
Period size: 32 Copynumber: 2.2 Consensus size: 31
17892 AGTGTTATAT
17902 TATATTTTAAAAATATTAATTAGTATATTTTAAA
1 TATATTTTAAAAATATTAATTAG-ATA--TTAAA
*
17936 TATATTTATTAAAATATTATATTA-ATATTAAA
1 TATATTT-TAAAAATATTA-ATTAGATATTAAA
17968 TATAT
1 TATAT
17973 AAATAATATT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
32 10 0.29
34 10 0.29
35 10 0.29
36 4 0.12
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (31 bp):
TATATTTTAAAAATATTAATTAGATATTAAA
Found at i:17973 original size:34 final size:33
Alignment explanation
Indices: 17902--17973 Score: 76
Period size: 34 Copynumber: 2.1 Consensus size: 33
17892 AGTGTTATAT
*
17902 TATATTTTAAAAATATTAATTAGTATATTTTAAA
1 TATATTTTAAAAATATTAATTAG-ATATTTAAAA
*
17936 TATATTTATTAAAATATTATATTA-ATA-TTAAATA
1 TATATTT-TAAAAATATTA-ATTAGATATTTAAA-A
17970 TATA
1 TATA
17974 AATAATATTA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
33 4 0.12
34 15 0.45
35 10 0.30
36 4 0.12
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (33 bp):
TATATTTTAAAAATATTAATTAGATATTTAAAA
Found at i:18035 original size:27 final size:26
Alignment explanation
Indices: 17964--18049 Score: 68
Period size: 27 Copynumber: 3.2 Consensus size: 26
17954 ATATTAATAT
*
17964 TAAATATATAAATAATATTATTCCTTA
1 TAAATA-ATAAATAATATTATTTCTTA
* * *
17991 TTAATAATTTAATGATATTATTTC-TA
1 TAAATAA-TAAATAATATTATTTCTTA
*
18017 TGAAATTAATAAATAATATAATTT-TTA
1 T-AAA-TAATAAATAATATTATTTCTTA
*
18044 TTAATA
1 TAAATA
18050 GTATATTATA
Statistics
Matches: 46, Mismatches: 9, Indels: 10
0.71 0.14 0.15
Matches are distributed among these distances:
25 2 0.04
26 6 0.13
27 35 0.76
28 3 0.07
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.48
Consensus pattern (26 bp):
TAAATAATAAATAATATTATTTCTTA
Found at i:18169 original size:21 final size:22
Alignment explanation
Indices: 18122--18178 Score: 55
Period size: 22 Copynumber: 2.6 Consensus size: 22
18112 TTTTATTATA
**
18122 ATATTAAAAATA-TAATAGTGT
1 ATATTAAAAATATTAATAGAAT
18143 ATTATTAAAAATATTAATA-AAT
1 A-TATTAAAAATATTAATAGAAT
**
18165 ATATTTTAAATATT
1 ATATTAAAAATATT
18179 TTAATAATTA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
21 12 0.40
22 13 0.43
23 5 0.17
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.44
Consensus pattern (22 bp):
ATATTAAAAATATTAATAGAAT
Found at i:18173 original size:23 final size:23
Alignment explanation
Indices: 18125--18195 Score: 65
Period size: 23 Copynumber: 3.1 Consensus size: 23
18115 TATTATAATA
* *
18125 TTAAAAATA-TAAT-AGTGTATT
1 TTAAAAATATTAATAAATATATT
18146 ATTAAAAATATTAATAAATATATT
1 -TTAAAAATATTAATAAATATATT
* * *
18170 TTAAATATTTTAATAATTAATATT
1 TTAAAAATATTAATAAAT-ATATT
18194 TT
1 TT
18196 GATTAAAATG
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
22 9 0.22
23 19 0.46
24 13 0.32
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.48
Consensus pattern (23 bp):
TTAAAAATATTAATAAATATATT
Found at i:20189 original size:19 final size:21
Alignment explanation
Indices: 20154--20192 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 21
20144 CATACAAATT
20154 TTAAACTTGTGAATTTTTGAG
1 TTAAACTTGTGAATTTTTGAG
20175 TTAAACTT-T-AATTTTTGA
1 TTAAACTTGTGAATTTTTGA
20193 TTTCAAATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 9 0.50
20 1 0.06
21 8 0.44
ACGTcount: A:0.31, C:0.05, G:0.13, T:0.51
Consensus pattern (21 bp):
TTAAACTTGTGAATTTTTGAG
Found at i:20685 original size:13 final size:13
Alignment explanation
Indices: 20646--20687 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
20636 ATTAAAAAAT
20646 ATATTTT-TATGA
1 ATATTTTATATGA
*
20658 AT-TTTTATATAA
1 ATATTTTATATGA
*
20670 ATATTTTATTTGA
1 ATATTTTATATGA
20683 ATATT
1 ATATT
20688 CAAAATTCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
11 4 0.16
12 8 0.32
13 13 0.52
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.60
Consensus pattern (13 bp):
ATATTTTATATGA
Found at i:23373 original size:14 final size:15
Alignment explanation
Indices: 23346--23375 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
23336 TATTTTAATT
23346 TTTAAAATTATTTTA
1 TTTAAAATTATTTTA
23361 TTTAAAA-TATTTTA
1 TTTAAAATTATTTTA
23375 T
1 T
23376 AAAAAAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
TTTAAAATTATTTTA
Found at i:23773 original size:31 final size:31
Alignment explanation
Indices: 23712--23778 Score: 82
Period size: 31 Copynumber: 2.1 Consensus size: 31
23702 TTAATTATTG
* *
23712 ACATGATATATATCACATCATCATATTAAAAT
1 ACATGATATATATCACAT-ATAATAATAAAAT
*
23744 ACATGTATATATATCATAT-TAATAATAAAAT
1 ACATG-ATATATATCACATATAATAATAAAAT
23775 ACAT
1 ACAT
23779 ATAAAAATAC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
31 14 0.45
32 5 0.16
33 12 0.39
ACGTcount: A:0.49, C:0.12, G:0.03, T:0.36
Consensus pattern (31 bp):
ACATGATATATATCACATATAATAATAAAAT
Found at i:32877 original size:25 final size:25
Alignment explanation
Indices: 32843--32890 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
32833 CACTCATTTA
*
32843 TAAAATAATATTTTATAAGAAATAGT
1 TAAAATAATATTTTA-AAAAAATAGT
32869 TAAAA-AATATTTTAAAAAAATA
1 TAAAATAATATTTTAAAAAAATA
32891 AATAATACAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.33
25 9 0.43
26 5 0.24
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.35
Consensus pattern (25 bp):
TAAAATAATATTTTAAAAAAATAGT
Found at i:35075 original size:30 final size:30
Alignment explanation
Indices: 35039--35102 Score: 110
Period size: 30 Copynumber: 2.1 Consensus size: 30
35029 GGCGTGAAAT
*
35039 ATAAACACGTCCATCTGAATCCATGCACTA
1 ATAAACACGTCCATCCGAATCCATGCACTA
*
35069 ATAAACACGTCCATCCGAATCTATGCACTA
1 ATAAACACGTCCATCCGAATCCATGCACTA
35099 ATAA
1 ATAA
35103 CCTTTATGCT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.39, C:0.28, G:0.09, T:0.23
Consensus pattern (30 bp):
ATAAACACGTCCATCCGAATCCATGCACTA
Found at i:37986 original size:48 final size:49
Alignment explanation
Indices: 37915--38042 Score: 159
Period size: 49 Copynumber: 2.6 Consensus size: 49
37905 GTGGTTTGAG
* * *
37915 TTAATTATGAATTGATCAAATTGTTACATCA-AAAGAAGGGTCACTGGA
1 TTAATTATAAATTGATCAAATTGTTACATCACAAAGAAGGATCACTGAA
* * * * *
37963 TTAATTATAAATCGATCAAATTGTTACACCACGAAGAAGGATTATTGAA
1 TTAATTATAAATTGATCAAATTGTTACATCACAAAGAAGGATCACTGAA
* *
38012 TTACTCATAAATTGATCAAATTGTTACATCA
1 TTAATTATAAATTGATCAAATTGTTACATCA
38043 TGAAGGATGG
Statistics
Matches: 67, Mismatches: 12, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
48 28 0.42
49 39 0.58
ACGTcount: A:0.41, C:0.12, G:0.14, T:0.33
Consensus pattern (49 bp):
TTAATTATAAATTGATCAAATTGTTACATCACAAAGAAGGATCACTGAA
Found at i:40932 original size:2 final size:2
Alignment explanation
Indices: 40925--40953 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
40915 AATCCAAATC
40925 AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
40954 TACAAGGTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Done.