Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001756.1 Hibiscus syriacus cultivar Beakdansim tig00003552_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: 59864
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.34
Found at i:1678 original size:28 final size:29
Alignment explanation
Indices: 1637--1702 Score: 91
Period size: 28 Copynumber: 2.3 Consensus size: 29
1627 AACACCCATA
1637 TTATCTTAACTTAAAAACATATTTTATTC
1 TTATCTTAACTTAAAAACATATTTTATTC
**
1666 TTAT-TTAACTTAAAATTATATTTTATT-
1 TTATCTTAACTTAAAAACATATTTTATTC
1693 TATATCTTAA
1 T-TATCTTAA
1703 ATTTTAAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 1 0.03
28 24 0.73
29 8 0.24
ACGTcount: A:0.38, C:0.09, G:0.00, T:0.53
Consensus pattern (29 bp):
TTATCTTAACTTAAAAACATATTTTATTC
Found at i:1722 original size:32 final size:31
Alignment explanation
Indices: 1677--1742 Score: 89
Period size: 32 Copynumber: 2.1 Consensus size: 31
1667 TATTTAACTT
1677 AAAATTATATTTTATTTATATCTTAAATTTTAA
1 AAAATTATATTTTATTTATAT-TT-AATTTTAA
* *
1710 AAAATTAT-TTTTATTTTTATTTTATTTTAA
1 AAAATTATATTTTATTTATATTTAATTTTAA
1740 AAA
1 AAA
1743 TCTTTAAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
30 10 0.32
31 2 0.06
32 11 0.35
33 8 0.26
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.58
Consensus pattern (31 bp):
AAAATTATATTTTATTTATATTTAATTTTAA
Found at i:1826 original size:30 final size:31
Alignment explanation
Indices: 1783--1860 Score: 88
Period size: 30 Copynumber: 2.5 Consensus size: 31
1773 ATAAATTAAG
*
1783 ATAAAATTATATTTTTAAAAGGT-ACATGATA
1 ATAAAA-TATATTTTTAAAAGGTCACATGAGA
* * *
1814 ATAAAATATA-TTTTAAAAGTTCATATTAGA
1 ATAAAATATATTTTTAAAAGGTCACATGAGA
*
1844 ATAAAATATGTTTTTAA
1 ATAAAATATATTTTTAA
1861 GTTAAAATAA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
29 10 0.25
30 18 0.45
31 12 0.30
ACGTcount: A:0.49, C:0.03, G:0.08, T:0.41
Consensus pattern (31 bp):
ATAAAATATATTTTTAAAAGGTCACATGAGA
Found at i:3597 original size:29 final size:29
Alignment explanation
Indices: 3565--3631 Score: 73
Period size: 30 Copynumber: 2.3 Consensus size: 29
3555 GACCAAAACT
*
3565 TAAATTTTGAAAGTTTAGTGGCCAAAGTA
1 TAAATTTTGAAAGTTTAGAGGCCAAAGTA
* * *
3594 TAAAGTTTGGAAATTTTAGAGTCCAAAGTA
1 TAAA-TTTTGAAAGTTTAGAGGCCAAAGTA
3624 -ATAATTTT
1 TA-AATTTT
3632 CTCAAAAAGA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
29 8 0.26
30 23 0.74
ACGTcount: A:0.39, C:0.06, G:0.18, T:0.37
Consensus pattern (29 bp):
TAAATTTTGAAAGTTTAGAGGCCAAAGTA
Found at i:4137 original size:15 final size:15
Alignment explanation
Indices: 4117--4147 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
4107 AGAAAAGTGT
4117 ATATGTTAATTATGA
1 ATATGTTAATTATGA
4132 ATATGTTAATTATGA
1 ATATGTTAATTATGA
4147 A
1 A
4148 GAGAAATCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.42, C:0.00, G:0.13, T:0.45
Consensus pattern (15 bp):
ATATGTTAATTATGA
Found at i:10612 original size:40 final size:40
Alignment explanation
Indices: 10557--10639 Score: 139
Period size: 40 Copynumber: 2.1 Consensus size: 40
10547 TTGTATGCTT
*
10557 GCAAAGGTATACAATATCAGGACTAACGAACATGATTTTG
1 GCAAAGGTATACAATATCAAGACTAACGAACATGATTTTG
* *
10597 GCAAAGGTATACAATATCAAGATTAACGAACATGGTTTTG
1 GCAAAGGTATACAATATCAAGACTAACGAACATGATTTTG
10637 GCA
1 GCA
10640 GAGGGAATAA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.40, C:0.14, G:0.20, T:0.25
Consensus pattern (40 bp):
GCAAAGGTATACAATATCAAGACTAACGAACATGATTTTG
Found at i:16838 original size:37 final size:37
Alignment explanation
Indices: 16789--16894 Score: 106
Period size: 37 Copynumber: 2.9 Consensus size: 37
16779 GTCAGAGTTG
* *
16789 GGTGG-AGAATATATATTTTTTGGGTCGGGTTGGGTTA
1 GGTGGAAG-ATATATAATTTTTGGGTCGGGTTGGGTCA
* * * * *
16826 GGTGGAAGATATATAATTTTCGAGTTGGGTCGGGTCG
1 GGTGGAAGATATATAATTTTTGGGTCGGGTTGGGTCA
* * *
16863 GGTGGAGGATGTATAAATTTTGGGTCGGGTTG
1 GGTGGAAGATATATAATTTTTGGGTCGGGTTG
16895 ACCAAAAACC
Statistics
Matches: 54, Mismatches: 14, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
37 52 0.96
38 2 0.04
ACGTcount: A:0.20, C:0.05, G:0.40, T:0.36
Consensus pattern (37 bp):
GGTGGAAGATATATAATTTTTGGGTCGGGTTGGGTCA
Found at i:32516 original size:73 final size:71
Alignment explanation
Indices: 32439--32602 Score: 154
Period size: 73 Copynumber: 2.2 Consensus size: 71
32429 ATCGATTTTT
* * * *
32439 AAAACTATGTTTTCAAAATTATATAATATATGTTTTTTAACAAATATTTTC-AAAAAC-ATATTA
1 AAAAC-AT-TTTTCAAAACTATATAATATATG-CTTTCAA-AAACATTTTCTAAAAACTATATTA
*
32502 TATATTTTCA
62 TACATTTTCA
* * *
32512 AAAACCAATTTTTAAAAACTATATATTATATGCTTTCAAAAACGTTTTCTAAAAACTATATATTA
1 AAAA-C-ATTTTTCAAAACTATATAATATATGCTTTCAAAAACATTTTCTAAAAAC--TATATTA
32577 TACATTTTCA
62 TACATTTTCA
32587 AAAA-ATATTTTCAAAA
1 AAAACAT-TTTTCAAAA
32603 ACTACATTAT
Statistics
Matches: 75, Mismatches: 10, Indels: 12
0.77 0.10 0.12
Matches are distributed among these distances:
71 8 0.11
72 13 0.17
73 32 0.43
74 3 0.04
75 19 0.25
ACGTcount: A:0.46, C:0.10, G:0.02, T:0.41
Consensus pattern (71 bp):
AAAACATTTTTCAAAACTATATAATATATGCTTTCAAAAACATTTTCTAAAAACTATATTATACA
TTTTCA
Found at i:32549 original size:38 final size:37
Alignment explanation
Indices: 32496--32606 Score: 127
Period size: 37 Copynumber: 3.0 Consensus size: 37
32486 TTTCAAAAAC
*
32496 ATATTATATATTTTCAAAAACCAATTTT-TAAAAACTAT
1 ATATTATATACTTTCAAAAA-C-ATTTTCTAAAAACTAT
* *
32534 ATATTATATGCTTTCAAAAACGTTTTCTAAAAACTAT
1 ATATTATATACTTTCAAAAACATTTTCTAAAAACTAT
* * *
32571 ATATTATACATTTTCAAAAAATATTTTC-AAAAACTA
1 ATATTATATACTTTC-AAAAACATTTTCTAAAAACTA
32607 CATTATATTA
Statistics
Matches: 63, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
36 4 0.06
37 31 0.49
38 28 0.44
ACGTcount: A:0.46, C:0.12, G:0.02, T:0.41
Consensus pattern (37 bp):
ATATTATATACTTTCAAAAACATTTTCTAAAAACTAT
Found at i:37800 original size:24 final size:24
Alignment explanation
Indices: 37790--37907 Score: 141
Period size: 24 Copynumber: 4.9 Consensus size: 24
37780 CATAATTCAC
* *
37790 GTCAAGTATCATATCAAAATCCAG
1 GTCAAGTATCAGATCAAAATCCAA
*
37814 GTCAAGTATCAGATCAGAATCCAA
1 GTCAAGTATCAGATCAAAATCCAA
* *
37838 GTCAAGTATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAAAATCCAA
*
37862 GTC-AGATATCAGATCAGAATCCATA
1 GTCAAG-TATCAGATCAAAATCCA-A
37887 -TCAAGTATCAGATCAGAAATC
1 GTCAAGTATCAGATCA-AAATC
37908 AAATCGAAAA
Statistics
Matches: 84, Mismatches: 6, Indels: 7
0.87 0.06 0.07
Matches are distributed among these distances:
23 2 0.02
24 76 0.90
25 6 0.07
ACGTcount: A:0.41, C:0.20, G:0.15, T:0.24
Consensus pattern (24 bp):
GTCAAGTATCAGATCAAAATCCAA
Found at i:37859 original size:48 final size:49
Alignment explanation
Indices: 37790--37904 Score: 173
Period size: 48 Copynumber: 2.4 Consensus size: 49
37780 CATAATTCAC
* *
37790 GTCAAGTATCATATCAAAATCCAGGTCA-AGTATCAGATCAGAATCCA-A
1 GTCAAGTATCAGATCAGAATCCAGGTCAGA-TATCAGATCAGAATCCATA
*
37838 GTCAAGTATCAGATCAGAATCCATGTCAGATATCAGATCAGAATCCATA
1 GTCAAGTATCAGATCAGAATCCAGGTCAGATATCAGATCAGAATCCATA
37887 -TCAAGTATCAGATCAGAA
1 GTCAAGTATCAGATCAGAA
37905 ATCAAATCGA
Statistics
Matches: 62, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
48 60 0.97
49 2 0.03
ACGTcount: A:0.41, C:0.20, G:0.16, T:0.23
Consensus pattern (49 bp):
GTCAAGTATCAGATCAGAATCCAGGTCAGATATCAGATCAGAATCCATA
Found at i:37921 original size:48 final size:48
Alignment explanation
Indices: 37766--37921 Score: 131
Period size: 48 Copynumber: 3.2 Consensus size: 48
37756 AAACGAATAT
* * * * * * * *
37766 ATCAAAAATCAAATCATAATTCACGTCAAGTATCATATCAAAATCCAG
1 ATCAGAAATCAGATCAGAATCCAAGTCAAGTATCAGATCAGAATCCAA
* * *
37814 GTCA-AGTATCAGATCAGAATCCAAGTCAAGTATCAGATCAGAATCCAT
1 ATCAGA-AATCAGATCAGAATCCAAGTCAAGTATCAGATCAGAATCCAA
* *
37862 GTCAGATATCAGATCAGAATCCATA-TCAAGTATCAGATCAGAAAT-CAA
1 ATCAGAAATCAGATCAGAATCCA-AGTCAAGTATCAGATCAG-AATCCAA
37910 ATC-GAAAATCAG
1 ATCAG-AAATCAG
37922 GTAAAATATT
Statistics
Matches: 91, Mismatches: 12, Indels: 10
0.81 0.11 0.09
Matches are distributed among these distances:
47 2 0.02
48 84 0.92
49 5 0.05
ACGTcount: A:0.44, C:0.20, G:0.13, T:0.23
Consensus pattern (48 bp):
ATCAGAAATCAGATCAGAATCCAAGTCAAGTATCAGATCAGAATCCAA
Found at i:37921 original size:72 final size:71
Alignment explanation
Indices: 37770--37921 Score: 164
Period size: 72 Copynumber: 2.1 Consensus size: 71
37760 GAATATATCA
* * * * *
37770 AAAATCAAATCATAATTCACGTCAAGTATCATATCAAAATCCAGGTCAAGTATCAGATCAGAATC
1 AAAATCAGATCAGAATCCACGTCAAGTATCAGATCAAAATCCAGATCAAGTATCAGATCAGAATC
*
37835 CAAGTC
66 CAAATC
* * * *
37841 AAGTATCAGATCAGAATCCATGTC-AGATATCAGATCAGAATCCATATCAAGTATCAGATCAGAA
1 AA-AATCAGATCAGAATCCACGTCAAG-TATCAGATCAAAATCCAGATCAAGTATCAGATCAG-A
37905 AT-CAAATC
63 ATCCAAATC
37913 GAAAATCAG
1 -AAAATCAG
37922 GTAAAATATT
Statistics
Matches: 66, Mismatches: 11, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
71 4 0.06
72 57 0.86
73 5 0.08
ACGTcount: A:0.44, C:0.20, G:0.13, T:0.23
Consensus pattern (71 bp):
AAAATCAGATCAGAATCCACGTCAAGTATCAGATCAAAATCCAGATCAAGTATCAGATCAGAATC
CAAATC
Found at i:40347 original size:13 final size:13
Alignment explanation
Indices: 40301--40354 Score: 54
Period size: 13 Copynumber: 3.8 Consensus size: 13
40291 AGTGGTCAAC
40301 GGTCAACGGGTCG
1 GGTCAACGGGTCG
* *
40314 GGTCTATGGGTCAGG
1 GGTCAACGGGTC--G
40329 TCGGTCAACGGGTCG
1 --GGTCAACGGGTCG
40344 GGTCAACGGGT
1 GGTCAACGGGT
40355 TAGGTTATGA
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
13 21 0.64
15 2 0.06
17 10 0.30
ACGTcount: A:0.15, C:0.20, G:0.44, T:0.20
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:44832 original size:40 final size:40
Alignment explanation
Indices: 44728--44883 Score: 228
Period size: 40 Copynumber: 4.0 Consensus size: 40
44718 ATCGATTAAG
*
44728 CACTTT-GTGCATATGGTAGGCATGACCTTATGTGTAATA
1 CACTTTGGTGCATATGGTAGGCACGACCTTATGTGTAATA
*
44767 CAC-TTAGTGCATATGGTAGGCACGACCTTATGTGTAATA
1 CACTTTGGTGCATATGGTAGGCACGACCTTATGTGTAATA
*
44806 CACTTTGGTGTATATGGT-GAGCACGACCTTATGTGTAATA
1 CACTTTGGTGCATATGGTAG-GCACGACCTTATGTGTAATA
* * *
44846 AACTTTGGTGCATATGGTGGGCGCGACCTTATGTGTAA
1 CACTTTGGTGCATATGGTAGGCACGACCTTATGTGTAA
44884 GCACTACAGT
Statistics
Matches: 107, Mismatches: 6, Indels: 7
0.89 0.05 0.06
Matches are distributed among these distances:
38 2 0.02
39 39 0.36
40 65 0.61
41 1 0.01
ACGTcount: A:0.25, C:0.16, G:0.26, T:0.33
Consensus pattern (40 bp):
CACTTTGGTGCATATGGTAGGCACGACCTTATGTGTAATA
Found at i:46891 original size:20 final size:20
Alignment explanation
Indices: 46854--46892 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
46844 AGAGCTCATA
* *
46854 TAGGATCATGTAGATGCATT
1 TAGGAGCATATAGATGCATT
*
46874 TAGGAGCATATAGTTGCAT
1 TAGGAGCATATAGATGCAT
46893 GTGGTGGAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.31, C:0.10, G:0.26, T:0.33
Consensus pattern (20 bp):
TAGGAGCATATAGATGCATT
Found at i:52779 original size:11 final size:11
Alignment explanation
Indices: 52763--52787 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
52753 GTTTAATTTG
52763 TTTTCTATTAC
1 TTTTCTATTAC
52774 TTTTCTATTAC
1 TTTTCTATTAC
52785 TTT
1 TTT
52788 ATATTCAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.16, G:0.00, T:0.68
Consensus pattern (11 bp):
TTTTCTATTAC
Found at i:54874 original size:20 final size:20
Alignment explanation
Indices: 54837--54875 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
54827 AGAGCTCATA
* *
54837 TAGGATCATGTAGATGCATT
1 TAGGAGCATATAGATGCATT
*
54857 TAGGAGCATATAGTTGCAT
1 TAGGAGCATATAGATGCAT
54876 GTGCTGGAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.31, C:0.10, G:0.26, T:0.33
Consensus pattern (20 bp):
TAGGAGCATATAGATGCATT
Done.