Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001380.1 Hibiscus syriacus cultivar Beakdansim tig00002693_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: 43202
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Found at i:159 original size:44 final size:45
Alignment explanation
Indices: 31--174 Score: 193
Period size: 45 Copynumber: 3.2 Consensus size: 45
21 AGAATCTTGA
* * *
31 TTAGAGAAGA-TGACAGAAGAAGAAAGAAGAAGGGAAGAGTCTCGA
1 TTAGAGAAGAGGGACAGAAGAAG-AAGAAGAATGGAAGAGTCTCGG
*
76 TTAGAGAAGAGGGACAGAAGAAGAAGAAGAATGGAAGAGTATCGG
1 TTAGAGAAGAGGGACAGAAGAAGAAGAAGAATGGAAGAGTCTCGG
* * *
121 TTAGAGAAGAGGGACATAA-AAGAATAATAATGGAAGAGTCTCGG
1 TTAGAGAAGAGGGACAGAAGAAGAAGAAGAATGGAAGAGTCTCGG
*
165 TTAGCGAAGA
1 TTAGAGAAGA
175 AGAACAAAAG
Statistics
Matches: 89, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
44 31 0.35
45 47 0.53
46 11 0.12
ACGTcount: A:0.47, C:0.06, G:0.33, T:0.14
Consensus pattern (45 bp):
TTAGAGAAGAGGGACAGAAGAAGAAGAAGAATGGAAGAGTCTCGG
Found at i:878 original size:2 final size:2
Alignment explanation
Indices: 873--901 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
863 TTAAAAAATA
873 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 A
902 AAAGTATATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:16133 original size:19 final size:19
Alignment explanation
Indices: 16106--16157 Score: 86
Period size: 19 Copynumber: 2.7 Consensus size: 19
16096 GAATGCAGTT
* *
16106 AGTGAATCGATGCATAAGG
1 AGTGCATCGATGCATAAGA
16125 AGTGCATCGATGCATAAGA
1 AGTGCATCGATGCATAAGA
16144 AGTGCATCGATGCA
1 AGTGCATCGATGCA
16158 CCCCCTTAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.35, C:0.15, G:0.29, T:0.21
Consensus pattern (19 bp):
AGTGCATCGATGCATAAGA
Found at i:16148 original size:83 final size:82
Alignment explanation
Indices: 16047--16223 Score: 225
Period size: 83 Copynumber: 2.1 Consensus size: 82
16037 TTCAGTGTGT
* *
16047 ATCGATGCACAGGAAGTGCATCGATGCA-CCCATTAAAAATGGAAACATCGAA-TGCAGTTAGTG
1 ATCGATGCACAAGAAGTGCATCGATGCACCCCATT-AAAATGAAAACATCGAAGTG-A-TTAGTG
16110 AATCGATGCATAAGG-AGTGC
63 AATCGATGCAT-AGGTAGTGC
* * * *
16130 ATCGATGCATAAGAAGTGCATCGATGCACCCCCTTAAAATGAAAACATCGAAGGTGATTGGTGTA
1 ATCGATGCACAAGAAGTGCATCGATGCACCCCATTAAAATGAAAACATCGAA-GTGATTAGTGAA
*
16195 TCGATGCATGGGTAGTGC
65 TCGATGCATAGGTAGTGC
16213 ATCGATGCACA
1 ATCGATGCACA
16224 TGTTAAATAA
Statistics
Matches: 82, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
82 2 0.02
83 72 0.88
84 6 0.07
85 2 0.02
ACGTcount: A:0.34, C:0.19, G:0.25, T:0.22
Consensus pattern (82 bp):
ATCGATGCACAAGAAGTGCATCGATGCACCCCATTAAAATGAAAACATCGAAGTGATTAGTGAAT
CGATGCATAGGTAGTGC
Found at i:18008 original size:21 final size:20
Alignment explanation
Indices: 17982--18020 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
17972 CAAGAGATTT
17982 CATCTCCAAACGGCTAGAAAA
1 CATCT-CAAACGGCTAGAAAA
*
18003 CATCTCTAACGGCTAGAA
1 CATCTCAAACGGCTAGAA
18021 CCGACCACAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.38, C:0.28, G:0.15, T:0.18
Consensus pattern (20 bp):
CATCTCAAACGGCTAGAAAA
Found at i:19273 original size:15 final size:15
Alignment explanation
Indices: 19241--19280 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
19231 GAAGATGATG
* *
19241 AAGAA-AAGAAAGAC
1 AAGAAGAAGGAAGAA
19255 AAGAAGAAGGAAGAA
1 AAGAAGAAGGAAGAA
19270 AAGAAGAAGGA
1 AAGAAGAAGGA
19281 GGTAGGCGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 5 0.22
15 18 0.78
ACGTcount: A:0.68, C:0.03, G:0.30, T:0.00
Consensus pattern (15 bp):
AAGAAGAAGGAAGAA
Found at i:21522 original size:20 final size:21
Alignment explanation
Indices: 21483--21522 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
21473 CAGAGATTTC
* *
21483 ATCCCCAAACGGGTATAAATT
1 ATCCCCAAACGGCTAGAAATT
21504 ATCCCC-AACGGCTAGAAAT
1 ATCCCCAAACGGCTAGAAAT
21523 AGCCACAACT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.38, C:0.28, G:0.15, T:0.20
Consensus pattern (21 bp):
ATCCCCAAACGGCTAGAAATT
Found at i:24885 original size:176 final size:177
Alignment explanation
Indices: 24582--24939 Score: 673
Period size: 176 Copynumber: 2.0 Consensus size: 177
24572 AGGAAGATAT
*
24582 TTATTGGCTAGCAGTCCACATATGATACCTTGTCAGTTGTGCCCCACACGTGAAGGGTATATTCC
1 TTATTGGCTAGCAGTCAACATATGATACCTTGTCAGTTGTGCCCCACACGTGAAGGGTATATTCC
24647 CTCAAGAATTAGGGCACAAAACCCTAGAAGCCCCCACTATATAAAGAAAAAGAACACCACATTTA
66 CTCAAGAATTAGGGCACAAAACCCTAGAAGCCCCCACTATATAAAGAAAAAGAACACCACATTTA
*
24712 TAGGAGGATGGAAAGTGTGAGATAAGAAAGAGAAAAACTAGAAGTGG
131 TAGGAGGATGAAAAGTGTGAGATAAGAAAGAGAAAAACTAGAAGTGG
24759 TTATTGGC-AGCAGTCAACATATGATACCTTGTCAGTTGTGCCCCACACGTGAAGGGTATATTCC
1 TTATTGGCTAGCAGTCAACATATGATACCTTGTCAGTTGTGCCCCACACGTGAAGGGTATATTCC
*
24823 CTCAAGAATTAGGGCACAAAACCCTAGGAGCCCCCACTATATAAAGAAAAAGAACACCACATTTA
66 CTCAAGAATTAGGGCACAAAACCCTAGAAGCCCCCACTATATAAAGAAAAAGAACACCACATTTA
*
24888 TAGGAGGATGAAAAGTGTGAGATAAGAAAGAGAAAAGCTAGAAGTGG
131 TAGGAGGATGAAAAGTGTGAGATAAGAAAGAGAAAAACTAGAAGTGG
24935 TTATT
1 TTATT
24940 CTTCTTTCTT
Statistics
Matches: 177, Mismatches: 4, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
176 169 0.95
177 8 0.05
ACGTcount: A:0.38, C:0.19, G:0.22, T:0.22
Consensus pattern (177 bp):
TTATTGGCTAGCAGTCAACATATGATACCTTGTCAGTTGTGCCCCACACGTGAAGGGTATATTCC
CTCAAGAATTAGGGCACAAAACCCTAGAAGCCCCCACTATATAAAGAAAAAGAACACCACATTTA
TAGGAGGATGAAAAGTGTGAGATAAGAAAGAGAAAAACTAGAAGTGG
Found at i:26983 original size:20 final size:20
Alignment explanation
Indices: 26960--27010 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
26950 CTATGCTAGA
26960 AGTATCGATACTATCTCTAT
1 AGTATCGATACTATCTCTAT
26980 AGTATCGATACTATCTCTAT
1 AGTATCGATACTATCTCTAT
*
27000 AGTATCAATAC
1 AGTATCGATAC
27011 CACATGAACA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.33, C:0.20, G:0.10, T:0.37
Consensus pattern (20 bp):
AGTATCGATACTATCTCTAT
Found at i:29057 original size:21 final size:20
Alignment explanation
Indices: 29033--29072 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
29023 TGTAGAGATT
29033 TCATCCCCAAACGGCTAGAAA
1 TCAT-CCCAAACGGCTAGAAA
*
29054 TCATCCCTAACGGCTAGAA
1 TCATCCCAAACGGCTAGAA
29073 CCACAACTCC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.35, C:0.33, G:0.15, T:0.17
Consensus pattern (20 bp):
TCATCCCAAACGGCTAGAAA
Found at i:35729 original size:16 final size:17
Alignment explanation
Indices: 35708--35741 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
35698 ATATTATCCG
35708 ATCCG-AAATTTCGGAT
1 ATCCGAAAATTTCGGAT
*
35724 ATCCGAAAATTTTGGAT
1 ATCCGAAAATTTCGGAT
35741 A
1 A
35742 CTTAAAGTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.32
Consensus pattern (17 bp):
ATCCGAAAATTTCGGAT
Found at i:41610 original size:47 final size:49
Alignment explanation
Indices: 41498--41628 Score: 142
Period size: 47 Copynumber: 2.7 Consensus size: 49
41488 CACCCGTAGA
* * * *
41498 AGTAAAGCGCGCCCCCTGAACCGCGCTATATGCTGATTTGGCACCACGTGG
1 AGTATAGCGCGCCCCCTGTACCGCGCTATACGCTGAGTT-G-ACCACGTGG
** *
41549 AGTATAGCTTGCCCCCTGTACCGCGCTATACGCTGGGTT-A-CACGTGG
1 AGTATAGCGCGCCCCCTGTACCGCGCTATACGCTGAGTTGACCACGTGG
*
41596 GGTATAGCGCGCCCCCTGCT-CCGCGCTATACGC
1 AGTATAGCGCGCCCCCTG-TACCGCGCTATACGC
41629 CACGTAGGGT
Statistics
Matches: 69, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
47 35 0.51
48 2 0.03
51 32 0.46
ACGTcount: A:0.18, C:0.34, G:0.27, T:0.21
Consensus pattern (49 bp):
AGTATAGCGCGCCCCCTGTACCGCGCTATACGCTGAGTTGACCACGTGG
Found at i:42403 original size:17 final size:17
Alignment explanation
Indices: 42375--42407 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
42365 TATTAATGTA
42375 TGAATCATTTATATTTTT
1 TGAATCATTTAT-TTTTT
42393 TGAAT-ATTTATTTTT
1 TGAATCATTTATTTTT
42408 AATAAGAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 6 0.40
18 5 0.33
ACGTcount: A:0.27, C:0.03, G:0.06, T:0.64
Consensus pattern (17 bp):
TGAATCATTTATTTTTT
Found at i:43078 original size:125 final size:130
Alignment explanation
Indices: 42855--43097 Score: 381
Period size: 125 Copynumber: 1.9 Consensus size: 130
42845 AATTTTCTTC
*
42855 TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGTTGACACATGTCAGAT
1 TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTGACACATGTCAGAT
** *
42920 CCTGGTTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
66 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAGCATATATAAA
*
42985 TAATTAGGTGGTGACATGTGTCACCAATGACA-AGTATC-TG-TCATGTGCT-A-ACAT-TCAGA
1 TAATTAGGTGGTGACATGTGTCACCAATAACACA-TATCATGATCATGTGCTGACACATGTCAGA
*
43044 TCCTAATTAAATGATTACTTTATTAAATTCTATTTAATTTAGGACCAAATTGAT
65 TCCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGAT
43098 TATATAAATA
Statistics
Matches: 106, Mismatches: 6, Indels: 7
0.89 0.05 0.06
Matches are distributed among these distances:
125 55 0.52
126 4 0.04
127 1 0.01
128 8 0.08
129 3 0.03
130 35 0.33
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.37
Consensus pattern (130 bp):
TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTGACACATGTCAGAT
CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAGCATATATAAA
Done.